Pokémon Platinum - It's one of the best games I've ever played, which means it's also the best Pokémon game I've played.
Pokémon Soul Silver - Not as good as Platinum, but there's nothing wrong with being close second.
Bowser's Inside Story - Should be evident.
Days of Ruin - Fantastic strategy game.
Dragon Quest V - Its sense of adventure is matched by very few games.
Yoshi's Island DS - Recently popped this in, and it's a lot better than I remember it being.
Contact - There's just something about this game.
Those are favorites, but I'm probably forgetting a couple.
Diddy Kong Racing DS - The original might not be perfect, but the remake is just awful. Despite being fueled with nitro-nostalgia, I still couldn't enjoy this game.
Pokémon White - I touched
upon my complaints in this thread
New Super Mario Bros. - For the same reasons as Pokémon White, but in the context of Mario games. Nothing more than a cash cow taking advantage of nostalgia.
Dragon Quest IX - Read the post I linked.
Rhythm Heaven - For literally the same reasons Cort mentioned. Damn that block-headed (both literally and figuratively) figure to hell.
Partners in Time - More or less of what the guy above me said.
Jump Ultimate Stars - So much for the hype. Seriously, Smash Bros. with a bunch of cool anime characters? (sure the stories and character development suck, but most of the characters are aesthetically cool.) Sounds awesome, but when I finally got around to playing it thanks to a friend who imported it, boy was I underwhelmed. I won't deny that part it was due to me overhyping it, but even with that in mind, the mechanics still suck.