Custer's Revenge: The Revenge!
E.T. for the PS3 360 and PC (because the graphics would be just too hardcore for the Wii).
Warcraft IV. Warcraft III is, to date, the best RTS game I've played, and if there's one franchise that could benefit from a fresh infusion of lore and characters, it's Warcraft. For those of you not familiar with the Warcraft universe, the latest expansion "Cataclysm" brings back Deathwing, a supervillian who has been thwarted so epically, even Bowser would nod in admiration of his determination.
Also, with the lore that's already in place, Warcraft IV has the potential for battles on a scale more epic than any yet witnessed in an RTS game. Four words: Titans versus Elder Gods. Awesome.
Okami 2. Okami (for the Wii) is one of my most favorite games of all time. Yes, yes, Okami is a LOT like Legend of Zelda. What of it? It's epic and grand with memorable characters, the lands you traverse are huge even when bounding along at top speed, the combat and controls are all but flawless; and to top it off, the final boss is more awesome than anything I've seen yet from LoZ. Sacrilege, I know, but that's how much I love this game.
That's why I think it deserves a sequel.... and also why I almost don't want one to happen. There's just no way a sequel could possibly live up to the divine greatness of the first one. The LoZ games have the advantage of not being direct sequels (in the entire series, there's been MAYBE two: Majora's Mask and Phantom Hourglass), something Okami couldn't have.
On the other hand, if it were perhaps something more like the pseudo-expansions that were made for Kingdom Hearts and Final Fantasy, that'd be more than adequate.
Gargoyle's Quest/Demon's Crest. Old-school platforming at its very finest. With Nintendo's resurgence of the old-school, complete with all the new DS and Wii games that are in 2.5D, including the much vaunted Metroid: Other M, Gargoyle's Quest/Demon's Crest would be absolutely perfect for showing off the glory of the old-school. Have I mentioned how delightfully old-school this stuff is? IT'S OLD-SCHOOL!
Mega Man X: Command Mission. An RPG set in the Mega Man X universe; it was grindy, short, had very little replay value, and random encounters were way, WAY to often. However, beneath that was a pretty solid JRPG with a story that I enjoyed, and at least a few things to distract you from the main game. I really think a well-executed sequel would make it go from just decent to really, really good.