For myself, if there's a game that has been re-released since (or before) and is better, or there's a substantially better (yet similar) sequel, I wouldn't consider it here.
For me, that axes RE4 (First edition PC with mods is incredible. It's a better offering than Capcom's HD version on PC), New Super Mario Bros. Wii (U is infinitely better, it makes Wii look like Metroid 1 compared to Super Metroid), Smash Bros. Brawl (I think everyone agrees Wii U and 3DS are significantly better, and maybe the best entries), Monster Hunter 3 (Wii U version blows it away), and Mario Kart Wii (Mario Kart 7 and 8 are widely considered to be significantly superior).
Super Mario Galaxy 2This game is quintessential. The first galaxy's only leg up over the sequel is the backstory of Rosalina. As for the game itself, Galaxy 2 is miles better.
Zack and Wiki: Quest for Barbaros' TreasureIt's a beautiful adventure game that got almost no love, even by people in the know. It's exceedingly well polished and thoughtfully designed. The game is also clever, extremely fun, and oozes personality. If this game had done better, I could see it as a legit branding franchise. It's extremely solid.
Tatsunoko vs CapcomIt's one of the only new fighting games on the system and it's a good one. Some like it more than Capcom's other fighting entries in the same generation of systems.
Metroid Prime TrilogySome people swear by these games, and as far as I know the Wii versions are definitive.
Punch-Out!!It's wonderful! I'm sad that it took so long to get a followup to Super Punch-Out!!
The Legend of Zelda: Twilight Princess/Skyward SwordIt's Zelda, it'll always be on my shelf.
Kirby's Epic YarnFortune StreetThis game is an absolute blast and a great game to play with others. There's some actual strategy involved in it as well.
Super Paper MarioIt's the weird one everyone hates, except me.
Fragile DreamsAdmittedly I've never finished this game, but when I had played it I was sucked in.
Games I would want to add, but haven't actually played much of: Last Story, Pandora's Tower, Xenoblade Chronicles, No More Heroes 2, MadWorld, and Little King's Story. Amongst others.