Psychonauts, for one. It's not a unique to be a Psychonauts fanboy as it used to be, but it's still an incredible game.
More than anything, I'm a fanboy of the incredible and much under-appreciated Chrono Cross. Easily my favorite game of all time, I've completed it many times in the last decade. It had a deep, twisting story, a 100% unique battle system, dozens of wildly varied characters to create your party out of, and a gorgeous, fully realized world to explore. Most people wrote it off as utter crap because it didn't continue the stroy from Chrono Trigger, but failed to realize that it was never meant to.