Portal and Minecraft. Neither of them were bad games, but Portal didn't deserve GOTY at all, even with the less than spectacular game releases of '07. Minecraft is just treated as art wherever I go and it seems like nothing but an average sandbox with crappy blocky graphics just to add nostalgic charm that suddenly makes the game amazing.
Oh, and every single Zelda title ever released, especially Majora's Mask. It's an above average series, but Nintendo beat the dead horse so much that the carcass is starting to rot, and now they both stink.