For the 2D systems (NES, SNES, Game Boy/Color/Advance) I second Ares. It's simple to use and it's nice to have a single program that can do all of them. Ares also supports N64, but it runs really hard on my computer, more so than the others. I'd recommend RMG then for N64. For GameCube/Wii, your best (only) option is Dolphin, which is really well made.