I've played with a crap ton of retro console emulators. Some are rather impressive, some aren't even worth a crap. After quite a lot of testing, here's my list of the consoles I consider to be the best- and worst-emulated. Note that this is mostly for Windows (where the best emulators reside, unless you build an emulation box) and some for PSP.
Best-Emulated Consoles
1-Tied) NES:
It's about as close as you can get to the real thing without actually doing such. Its compatibility list is near perfect and it has every setting one can wish for, scanlines included. There's really not much to say about this one since it's so good. The hands-down best NES emulator is NESter on Windows and NESterJ on PSP.
1-Tied) Atari 2600:
Same as NES, but I believe this is the only perfect emulator. It claims to have 100% compatibility, and while I didn't have the patience to actually test every one of the 2600's games, others apparently have. I haven't found a single person complain about emulating the 2600 (apart from the nature of emulators, but that's another topic). The best emulator, in my opinion, is Stella for Windows 64-bit, although I haven't come across any problems on the PSP.
3) GameBoy/GameBoy Color:
Definitely up there, the GB/GBC emulators work quite well. Being compatible with nearly every game to exist on these consoles, these also tend to give a wide range of settings to adapt the games to whatever rig (or PSP) you have. The thing that's annoying with these emulators, however, is the stretching that the games go through on Windows. You're just gonna have to play in Windowed Mode to get the best picture possible. I've had no problem running Bgp on Windows, but any decent GB/GBC emulator's best on the PSP (GEmp is popular, but I have Homer's RIN on PSP)
4) Gamecube/Wii:
Surprisingly VERY good! If you can hook up a sensor bar to your computer, get a USB Gamecube controller/bluetooth Wavebird, and your computer just so happens to have bluetooth capabilities, you're gonna have a good time. The ONLY reason that I have this under the GB/GBA is due to the resources it requires to run, as well as getting the shit to actually play with it; there's no way you're just going to have a sensor bar that'll hook up to your computer laying around. Besides all of that, it has excellent compatibility across the board and various settings to play the games as you please. Hell, you can play Xenoblade Chronicles in glorious 1080p! Don't believe me? Here!
Beautiful.
The hands-down best emulator for Gamecube/Wii is Dolphin, which was originally a Gamecube emulator. However, the Wii hardware was basically a beefier version of the Gamecube's, so the conversion was quite easy. It's also open-platform I believe, so it's constantly getting updates.
5) GameBoy Advance:
I had to put this separate from GB/GBA because of various issues I've run into with either compatibility or performance. No GBA emulator I've tested actually runs perfectly. On my computer, I sometimes run into snags, strange slowdown, or freezing. On the PSP, it's the same thing. However, that's more than I can say for a crap ton of emulators for other consoles. The very best GBA emulator out there is VisualBoyAdvance for Windows, but its unofficial port for the PSP isn't worth a damn. I run gpSP Kai on PSP instead.
6-Tied) SNES:
Same as the GBA emulators, except the compatibility is nowhere near as good, especially with emulating the FX chip. This problem is somewhat mitigated on Windows, but I can barely play FX games on the PSP without performance issues. No one SNES emulator gets perfect compatibility, but it's generally decent. Playing with the settings in order to get it to work decently is a chore. The best Windows emulator is ZSNES (there's a version with NetPlay), while the best one on PSP is the SNES9X port (called SNES9X TYL). The Windows version is far better.
6-Tied) Nintendo 64:
The N64 emulators I've tried are rather decent, but good lord are they a chore to run correctly. There's many plugins that you have to get in order to run it the way you want it to, configurations for a variety of different ways to play, and the occasional bug (yes, this is where the bugs start occurring). Even after all of that bullshit is done and over with, you still have to deal with the half-decent compatibility for these emulators. With all of that said, if you do manage to get a game running right on Windows, it'll run right. Until you run into a bug, it'll be just fine. The most up-to-date emulator for Windows is Project64. Don't even bother with the PSP.
Honorable Mentions: Famicom, Neo-Geo Pocket Color, MAME, Capcom Play Station 1/2/3
Worst-Emulated Consoles:
1-Tied) PS2:
Tied for single-worst console to ever emulate on a computer, the compatibility is EXTREMELY poor for the PS2 library, and it takes a surprisingly high amount of resources to run the shit (even for multi-core usage). In fact, this takes the highest amount of resources to run out of any emulator. Playing with the settings will take up more time than playing with the actual games, and it's a chore to even get the games to run properly. You'd think that the PS2, being a system that's weaker than every decent computer released since 2005, wouldn't be such a hassle to run. It is. If you wanna give it a go, try PCSX2. Other options include buying a PS2 or hacking a PS3, both of which saves you a headache.
1-Tied) Sony PSP:
Holy balls, I don't know what's worse- having one classic system run horribly on a decent computer or another classic system run horribly on a decent computer. Just explaining the situation of this emulator puts into perspective how shitty this actually is: an emulator for one of the most innovative handhelds of all time running poorly on a computer that has four times its processing power. Couldn't make it up if I tried. Shitty compatibility, shitty performance, shitty bugs, shitty UI, shitty shitty shitty. Don't try it. Besides, emulating a PSP on PC is quite redundant, seeing as though the PSP isn't a half-bad emulation console. If you're a masochist or just wanna spite me, then look up PPSSPP.
3) SEGA Dreamcast:
I'm just gonna say this right now- you're gonna see a lot of SEGA systems in this section. The Dreamcast, however, tops them. The only reason it's under the PSP is that it actually has somewhat decent compatibility. That's the only compliment I can give it though. The UI is generally confusing, and your favorite game on these types of emulators will be "Settings." Not much to say here. The "best" emulator is Chankcast on Windows. Just get a Dreamcast. Don't waste your time.
4-Tied) SEGA Genesis:
To the emulator programmers' credit, the Genesis is a very hard console to actually replicate. There aren't even that many 3rd party retro consoles that run the actual carts properly. The only one that comes close is the RetroN 3, which is definitely the best way to play Genesis games without the actual Genesis. These emulators, however, are years behind the RetroN 3. They don't boast the same compatibility, and they're a chore to run properly. Don't waste your time. If you do wanna waste your time, get Fusion. If you don't, just get a RetroN 3. It comes with S-video output AND costs less than the S-video mod for a Genesis.
4-Tied) SEGA Saturn:
Definitely not even worth the time to get it running properly, which is a hassle. The compatibility is somehow worse than the Genesis emulators, and it takes a surprising high amount of resources to run. Not worth the time. SSF half-works if you wanna try.
6) Nintendo Virtual Boy:
Yes, it exists. Red Dragon is a Virtual Boy emulator. It works decently and has 100% compatibility! That's by default, since you can hold all of the Virtual Boy games in one hand. So why's it here? Who the hell actually wants a Virtual Boy emulator? The only thing I'm giving it credit for is actually getting the Virtual Boy games away from one's eyes a little more. That's all.
Honorable Mentions: Xbox (only runs Halo), Panasonic 3D0, Phillips CD-i
An Emulated Console that's About as Middle-of-the-Road as One Possibly Gets:
Sony Playstation:
Yep, this is about as close to the median as these emulators go. I'd have it in the "Best-Emulated" section if it weren't such a pain in the ass and buggy. I'd have it in the "Worst-Emulated" section if it weren't for its surprising compatibility range and advantages it brings. However, I'm only referring to one emulator, and it's not ePSXe. ePSXe is the most popular Playstation emulator, but why that is is beyond me. It has SO many bugs and runs quite poorly, not to mention it's so much of a pain to operate; you literally need a separate configuration for each game to run properly. No. Arbex/Xebra is the best Playstation emulator, no competition. It comes in two parts:
-Arbex: the "true-to-console" emulation bit. This part seeks to operate as closely to the Playstation as possible, which it actually does a decent job of. However, it's not exactly that stunning, considering it doesn't really run as closely to the console as advertised. You're better off getting an actual Playstation. It's at least better than xPSXe.
-Xebra: now we're talkin'! This is the "enhanced" emulation bit, which, in my opinion, is what truly distinguishes the emulator from an actual console. Using the power of your futuristic computing technology, you can have the smoothest, best-looking Playstation games of all time. You can even eliminate long loading screens! All of this while having a great compatibility range! Not bad! Bugs truly are the only thing ruining this. Once those have been ironed out, however, I'd consider running Xebra on your rig up there with just modding a PS2 or PS3 to run Playstation games. Or course, if you'd like something that's capable of running everything ever released on Sony's consoles, a modded PS3 won't disappoint. PS4's rather young, so I'd say wait on that.
I didn't include the old computer emulators because they all generally run nicely, so it would've been futile to lump them in with the console emulators.
I really hate it when programmers release Alpha or even Beta versions of their emulators when they're not open-platform. It's truly a wonder as to why the hell the emulation communities actively defend this shit. "It can get better, bro!" "Well, why don't you make YOUR OWN or even HELP?!" What, was my brother supposed to make his own console and controller when both his Xbox 360 and controller failed him? Gimmie a break...
Also, they have a tendency to shoot down collectors and the actual retro consoles, as if they're "saving gamers from the tyranny of the market." The fact that there's a market for these items is a GOOD thing.
1-Tied) NES:
It's about as close as you can get to the real thing without actually doing such. Its compatibility list is near perfect and it has every setting one can wish for, scanlines included. There's really not much to say about this one since it's so good. The hands-down best NES emulator is NESter on Windows and NESterJ on PSP.
1-Tied) Atari 2600:
Same as NES, but I believe this is the only perfect emulator. It claims to have 100% compatibility, and while I didn't have the patience to actually test every one of the 2600's games, others apparently have. I haven't found a single person complain about emulating the 2600 (apart from the nature of emulators, but that's another topic). The best emulator, in my opinion, is Stella for Windows 64-bit, although I haven't come across any problems on the PSP.
3) GameBoy/GameBoy Color:
Definitely up there, the GB/GBC emulators work quite well. Being compatible with nearly every game to exist on these consoles, these also tend to give a wide range of settings to adapt the games to whatever rig (or PSP) you have. The thing that's annoying with these emulators, however, is the stretching that the games go through on Windows. You're just gonna have to play in Windowed Mode to get the best picture possible. I've had no problem running Bgp on Windows, but any decent GB/GBC emulator's best on the PSP (GEmp is popular, but I have Homer's RIN on PSP)
4) Gamecube/Wii:
Surprisingly VERY good! If you can hook up a sensor bar to your computer, get a USB Gamecube controller/bluetooth Wavebird, and your computer just so happens to have bluetooth capabilities, you're gonna have a good time. The ONLY reason that I have this under the GB/GBA is due to the resources it requires to run, as well as getting the shit to actually play with it; there's no way you're just going to have a sensor bar that'll hook up to your computer laying around. Besides all of that, it has excellent compatibility across the board and various settings to play the games as you please. Hell, you can play Xenoblade Chronicles in glorious 1080p! Don't believe me? Here!
Beautiful.
The hands-down best emulator for Gamecube/Wii is Dolphin, which was originally a Gamecube emulator. However, the Wii hardware was basically a beefier version of the Gamecube's, so the conversion was quite easy. It's also open-platform I believe, so it's constantly getting updates.
5) GameBoy Advance:
I had to put this separate from GB/GBA because of various issues I've run into with either compatibility or performance. No GBA emulator I've tested actually runs perfectly. On my computer, I sometimes run into snags, strange slowdown, or freezing. On the PSP, it's the same thing. However, that's more than I can say for a crap ton of emulators for other consoles. The very best GBA emulator out there is VisualBoyAdvance for Windows, but its unofficial port for the PSP isn't worth a damn. I run gpSP Kai on PSP instead.
6-Tied) SNES:
Same as the GBA emulators, except the compatibility is nowhere near as good, especially with emulating the FX chip. This problem is somewhat mitigated on Windows, but I can barely play FX games on the PSP without performance issues. No one SNES emulator gets perfect compatibility, but it's generally decent. Playing with the settings in order to get it to work decently is a chore. The best Windows emulator is ZSNES (there's a version with NetPlay), while the best one on PSP is the SNES9X port (called SNES9X TYL). The Windows version is far better.
6-Tied) Nintendo 64:
The N64 emulators I've tried are rather decent, but good lord are they a chore to run correctly. There's many plugins that you have to get in order to run it the way you want it to, configurations for a variety of different ways to play, and the occasional bug (yes, this is where the bugs start occurring). Even after all of that bullshit is done and over with, you still have to deal with the half-decent compatibility for these emulators. With all of that said, if you do manage to get a game running right on Windows, it'll run right. Until you run into a bug, it'll be just fine. The most up-to-date emulator for Windows is Project64. Don't even bother with the PSP.
Honorable Mentions: Famicom, Neo-Geo Pocket Color, MAME, Capcom Play Station 1/2/3
Worst-Emulated Consoles:
1-Tied) PS2:
Tied for single-worst console to ever emulate on a computer, the compatibility is EXTREMELY poor for the PS2 library, and it takes a surprisingly high amount of resources to run the shit (even for multi-core usage). In fact, this takes the highest amount of resources to run out of any emulator. Playing with the settings will take up more time than playing with the actual games, and it's a chore to even get the games to run properly. You'd think that the PS2, being a system that's weaker than every decent computer released since 2005, wouldn't be such a hassle to run. It is. If you wanna give it a go, try PCSX2. Other options include buying a PS2 or hacking a PS3, both of which saves you a headache.
1-Tied) Sony PSP:
Holy balls, I don't know what's worse- having one classic system run horribly on a decent computer or another classic system run horribly on a decent computer. Just explaining the situation of this emulator puts into perspective how shitty this actually is: an emulator for one of the most innovative handhelds of all time running poorly on a computer that has four times its processing power. Couldn't make it up if I tried. Shitty compatibility, shitty performance, shitty bugs, shitty UI, shitty shitty shitty. Don't try it. Besides, emulating a PSP on PC is quite redundant, seeing as though the PSP isn't a half-bad emulation console. If you're a masochist or just wanna spite me, then look up PPSSPP.
3) SEGA Dreamcast:
I'm just gonna say this right now- you're gonna see a lot of SEGA systems in this section. The Dreamcast, however, tops them. The only reason it's under the PSP is that it actually has somewhat decent compatibility. That's the only compliment I can give it though. The UI is generally confusing, and your favorite game on these types of emulators will be "Settings." Not much to say here. The "best" emulator is Chankcast on Windows. Just get a Dreamcast. Don't waste your time.
4-Tied) SEGA Genesis:
To the emulator programmers' credit, the Genesis is a very hard console to actually replicate. There aren't even that many 3rd party retro consoles that run the actual carts properly. The only one that comes close is the RetroN 3, which is definitely the best way to play Genesis games without the actual Genesis. These emulators, however, are years behind the RetroN 3. They don't boast the same compatibility, and they're a chore to run properly. Don't waste your time. If you do wanna waste your time, get Fusion. If you don't, just get a RetroN 3. It comes with S-video output AND costs less than the S-video mod for a Genesis.
4-Tied) SEGA Saturn:
Definitely not even worth the time to get it running properly, which is a hassle. The compatibility is somehow worse than the Genesis emulators, and it takes a surprising high amount of resources to run. Not worth the time. SSF half-works if you wanna try.
6) Nintendo Virtual Boy:
Yes, it exists. Red Dragon is a Virtual Boy emulator. It works decently and has 100% compatibility! That's by default, since you can hold all of the Virtual Boy games in one hand. So why's it here? Who the hell actually wants a Virtual Boy emulator? The only thing I'm giving it credit for is actually getting the Virtual Boy games away from one's eyes a little more. That's all.
Honorable Mentions: Xbox (only runs Halo), Panasonic 3D0, Phillips CD-i
An Emulated Console that's About as Middle-of-the-Road as One Possibly Gets:
Sony Playstation:
Yep, this is about as close to the median as these emulators go. I'd have it in the "Best-Emulated" section if it weren't such a pain in the ass and buggy. I'd have it in the "Worst-Emulated" section if it weren't for its surprising compatibility range and advantages it brings. However, I'm only referring to one emulator, and it's not ePSXe. ePSXe is the most popular Playstation emulator, but why that is is beyond me. It has SO many bugs and runs quite poorly, not to mention it's so much of a pain to operate; you literally need a separate configuration for each game to run properly. No. Arbex/Xebra is the best Playstation emulator, no competition. It comes in two parts:
-Arbex: the "true-to-console" emulation bit. This part seeks to operate as closely to the Playstation as possible, which it actually does a decent job of. However, it's not exactly that stunning, considering it doesn't really run as closely to the console as advertised. You're better off getting an actual Playstation. It's at least better than xPSXe.
-Xebra: now we're talkin'! This is the "enhanced" emulation bit, which, in my opinion, is what truly distinguishes the emulator from an actual console. Using the power of your futuristic computing technology, you can have the smoothest, best-looking Playstation games of all time. You can even eliminate long loading screens! All of this while having a great compatibility range! Not bad! Bugs truly are the only thing ruining this. Once those have been ironed out, however, I'd consider running Xebra on your rig up there with just modding a PS2 or PS3 to run Playstation games. Or course, if you'd like something that's capable of running everything ever released on Sony's consoles, a modded PS3 won't disappoint. PS4's rather young, so I'd say wait on that.
I didn't include the old computer emulators because they all generally run nicely, so it would've been futile to lump them in with the console emulators.
I really hate it when programmers release Alpha or even Beta versions of their emulators when they're not open-platform. It's truly a wonder as to why the hell the emulation communities actively defend this shit. "It can get better, bro!" "Well, why don't you make YOUR OWN or even HELP?!" What, was my brother supposed to make his own console and controller when both his Xbox 360 and controller failed him? Gimmie a break...
Also, they have a tendency to shoot down collectors and the actual retro consoles, as if they're "saving gamers from the tyranny of the market." The fact that there's a market for these items is a GOOD thing.