Bsnes is the most accurate and compatible SNES emulator and will probably always be because there's literally not much more to improve on... atleast nothing the human eye can detect. So if you have a powerful enough computer to run it, it's the way to go. If you have an older computer, than Snes9X is your next best option.
Nintendulator is the most accurate NES emulator. Nestopia is also extremely accurate. But Nintendulator is basic with very few features. Nestopia is the most compatible NES emulator. Nestopia is extremely accurate and if you just want to play games it has the most features, eye candy, options, etc. than any other NES emulator in terms of gameplay. Meaning, if you just want to play NES games, than Nestopia is the way to go. BUT, if you are interested in TAS videos, recording playthroughs, recording sound/music, hacking cheat codes, etc. than FCEUX is by far the way to go. FCEUX is probably the best emulator ever made to hack cheat codes with.
Kega Fusion is the best Sega Genesis, Master System, Game Gear, 32X, and Sega CD emulator. But if you are interested in TAS video stuff such as recording videos/music, etc. than "Gens-rr" is the way to go. If you want to hack cheat codes, use "Gens 2.10 Hacking Version" or MESS.
Stella is the best Atari 2600 emulator.
ParaJVE is a good Vectrex emulator.
VBA-M and VBA-rr are the best Game Boy, Game Boy Color, and Game Boy Advance emulators. They are both branches of the original VBA (Visual Boy Advance.) VBA-M and VBA-rr are very similiar with slight differences... such as VBA-rr is more equipped to do TAS video stuff.
As for the TurboGrafX-16, if you don't like Magic Engine... try "Ootake". Ootake has more features and abilities than Magic Engine.
I don't know alot about MESS but I like it's goal. It's only going to improve over time too. Currently, MESS is probably very good to use for old, obscure game consoles. I'm sure somebody with more knowledge of MESS could inform you which game systems is the best to use it for.
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My favorite emulator out of every game console is Nestopia. It has everything that I could possibly want. The main things that I like about it is:
HQ4X Video Filter Ability to map any feature, key, button, etc. to the gamepad. Fast Foward support Rewind support Most compatible NES emulator Extremely Accurate
I have a Playstation 1 type USB controller (Steel Series 1G USB Controller) that I use. The following is how I map it in Nestopia:
L2 button = Save State R2 button = Load State L1 button = Rewind R1 button = Fast Foward Triangle button = Pauses emulator
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