NES: I've only use FCE Ultra, and it's worked perfectly: 100% so I haven't tried anything else.
SNES: Snes9X has good resolution and support for the number pad keys, but ZSNES is more compatible and sounds better.
Game Boy Color: REW is really good, and TGB-Dual is as good but allows two linked gameboys.
N64: Project 64 is the most compatible emulator yet! Gotta love Project64
Game Boy Advance: I haven't tried many yet, but DreamGBA works fine, except for a DOS-like feel to it.