Emulators

Nintendo
FCE Ultra My preferred NES Emulator.
Rock NES Another good emulator for NES games.

SNES
Snes9x My preferred SNES Emulator.
ZSNES Another good emulator for SNES games.

N64
Project 64 My preferred N64 Emulator.
1964 Another good emulator for N64 games. Can play some games PJ64 can not.

Gameboy
Visual Boy Advance v. 1.8.0 beta 3 My preferred emulator. I play all my games on here except the Legacy of Goku of course. :o) With this newest version you can play the Hamtaro Ham-Ham Heartbreak game.
Visual Boy Advance v. 1.1 You will need this older version of VBA in order to play DBZ The Legacy of Goku game and Buu's Fury.
Boycott Second best emulator. Only drawback is no full screen mode.
Rew This one was the only one I played until I found Visual Boy. It doesn't have a Gameshark.
GBEmu This one emulates the Gameboy entirely. It starts up like the real one does, has the same color screen as it and everything.
Smygb Another good emulator to check out.
NO$GBA NO$GBA started as a Gameboy Advance debugger but was later released as a normal emulator(version 1.9). It is the first gameboy advance emulator to support multiplayer games on the same pc!