Yes, fceu has joystick support. My Nyko works perfectly. Fceu Ultra is really nice, it even supports mapper 5 for Castlevania 3.
For GB/GBA, Visualboyadvance with the Gnomeboyadvance frontend is a nice combo.
For SNES, ZSNES is very nice.
For N64, Mupen64 is good.
I have a TV card for my Cube so now my computer can play just about everything Nintendo ever did. Maybe there will be a DS emu soon?