My personal favourites:
NES - FCEUX (Nestopia doesn't play headerless ROMS but is slightly more accurate)
SNES - Snes9x (if you have a good PC, use bsnes/higan)
N64 - Mupen64Plus (command line only in the latest version since the Python-based UI is broken in 2.5)
GCN - Dolphin (no other choice)
GB - TGB Dual (just like this one)
GBA - VisualBoyAdvance-M (continuation of VBA)
DS - DeSmuME (accurate and almost as fast as nocash)
I haven't really used many other console emulations I'll update more though when I play more in Sega and Atari stuff.
My hard drive corrupted itself a few days ago along with all my games for some reason so I'll need to test things again now.
You might want to look elsewhere for Mac/Linux stuff, though.
~Cammy