I run MAME plus the key 90's SEGA/Nintendo consoles.
SNES - ZSNES
Megadrive - KEGA Fusion
NES - FCEUltra
Master System - KEGA Fusion
Gameboy/Colour - BGB
Game Gear - KEGA Fusion
Nintendo consoles are mildly more complex, which is why there was never one good emulator for all. KEGA Fusion though is a brilliant Multi-SEGA emulator so if you wanted more (32x, Mega-CD) it shouldn't be too hard to configure. Personally I just stick with these as they are the consoles I grew up with, and represent the best amount of games for limited space.