The Wii U's virtual console hasn't gotten N64 games yet, which is odd. It would be convenient to be able to use the Wii U's features while playing an N64 VC game like save states and being able to use the internet browser while in-game. My guess is that they may have to do some extra emulation for N64 games (as I'm sure the mostly-2D games of the NES, SNES, and GBA are easier to emulate with the added Wii U features) and haven't finalized what the emulation will be yet.
Anyway for me.
N64:
Donkey Kong 64 (main issue is the Jetpak minigame as Microsoft owns the IP now, so if they could somehow alter the code to change it with, say, DK Jr then they may be able to get it on there)
Body Harvest (from the makers of GTA, it's a cool open world-like sci-fi game)
Turok 1, 2, and 3 (Disney bought the IP after Akklaim went under, so they'd have to be the ones to talk to about this one)
Gamecube:
F-Zero GX (I actually never played this)
Viewtiful Joe 1 and 2 (surprised Capcom hasn't just done some HD Collection yet)
Eternal Darkness (still own it, but wouldn't mind re-buying)
Fire Emblem: Path of Radiance (also never played this)
That's all I've got for now.