SNES9x based SNES emus are great. All the others have a few issues with them, I've found. ZSNES, for example, has some really clunky design and CPU hog issues. ...As a matter of fact (while I'm on the subject) most emus have some absolute shit code in them--probably why they get project-split so much. The worst offenders in this regard are probably gens, epsxe, and desmume. I actually spent an afternoon once re-writing the opengl (peops IIRC) plugin for epsxe and got over 800% speed increase a few years back. I tried the same once for desmume but after extensive profiling it turned out to be a more complex threading problem (that eats up huge chunks of time all together) so I just deleted it.
My favorite emulators would have to be
-Snes9x+
-PSX (1.13+)
-ppsspp
Obviously there's a load of great NES emulators as well.
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