Here is what I run, and seems to work well:
Sega Genesis - Fusion (also does SMS, SegaCD, and 32X)
NES - Nestopia or FCEUX
N64 - I haven't found one that I'm happy with. PJ64 is probably the best bet at this point. MESS made some good progress a few months ago, but it just hit a wall.
Atari 2600 - Stella
Commodore 64 - VICE