N64 by far... except most the games I'd like to see aren't Nintendo's IP.
Majora's Mask, Mario 64, Mario Kart 64 (IMO still the best mario kart), Jet Force Gemini, Mischief Makers, Goldeneye 007, Perfect Dark, Banjo Kazooie 1 + 2, Doom 64 (don't know why, always been fond of this version of Doom), and Tetrisphere would be amazing in 3D.
For gamecube, there's really just Melee, Wind Waker and Phantasy Star Online Episode I + II Plus.
I really don't understand why people are thinking that Wii U is going to get GCN VC. Do you people really think that Nintendo is suddenly going to start listing 500 MB+ games for download after all the problems they had with WiiWare being even 100 MB?
As for the topic, neither. I want sequels. Eternal Darkness 2: Sanity's Respite 3DS, please.