RockNES X (2.0 beta2) is my favorite.  It's based on the DOS-based RockNES.
FCE Ultra (0.50) is an excellent emulator with adjustable video modes and Game Genie support.

ZNES (1.36) is a great DOS-based emulator that supports triple-buffering and various video modes.
Snes9x (1.42) is another good emulator that supports all the popular "rendering" modes.

Project64 (1.4) is a somewhat complex, but robust emulator for the Nintendo 64.

VisualBoyAdvance (1.5.1) plays all Game Boy, Game Boy Color and Game Boy Advance games.

Gens (2.11) includes lots of rendering modes to smoothen edges and plays MD, Mega-CD and 32X games.

Meka (0.65c) is a very nice emulator that plays Master System as well as Mark III, Game Gear and other games.