I do want GameCube games on the Wii U Virtual Console, but before that I wish they would get more SNES and N64 games on the service (especially considering the Wii U Virtual Console won't even be launching with N64 games). Most notably, we're still missing notable SNES games from Square-Enix, and I don't care what Nintendo has to do to get them: Lufia 1 & 2, Illusion of Gaia, and Terranigma.
We're also still missing the original Star Fox, Earthbound, and Yoshi's Island from Nintendo, which Nintendo could probably figure out how to get working via emulation if they really gave a damn about the VC.
If Disney is feeling more generous these days about re-releasing their old games, I'd like to get both versions of Aladdin and The Lion King on the SNES/Genesis. There's also all the old Capcom Disney games on the NES, but those are probably being held for HD remakes pending the success or failure of the DuckTales remake.
Unfortunately, once you reach the N64 and GameCube, the most interesting games I'd like to see are from 3rd parties, and they've been the most reluctant to support VC. For instance, I'd like to see Castlevania: Legacy of Darkness and Hybrid Heaven N64 games from Konami. We also have 4 Rare N64 games and one GameCube game that seem to be in some kind of limbo right now that Nintendo may still hold the rights to re-release: Blast Corps, Jet Force Gemini, Diddy Kong Racing, Donkey Kong 64 (yes, for all its many faults I did like that game back in the day), and Star Fox Adventures.
On the GameCube side, I'd definitely like to see Skies of Arcadia Legends get released on VC from SEGA. There's also Silicon Knights' Eternal Darkness, Namco-Bandai's Tales of Symphonia, and both of Monolith's Baten Kaitos games. And that's just a start on the GameCube side.
On a sidenote, these games are a big question mark right now because of the whole debacle with the fall of LucasArts, but I'd like to get the two Rogue Squadron games + Battle for Naboo on VC. The VC version of Rogue Leader would require some retooling to get around the Wii U not having analog shoulder triggers, but it should be possible.