Since most of what I'd have listed are already present (Psychonauts, Lode Runner, etc), I think I'll go with Crackdown. I absolutely adore that game. I know most people that bought it only did so to get the Halo 3 beta. After which time, they immediately sold the game. Granted, I know most gamers aren't fans of sandbox games (and no, GTA DOES NOT COUNT), and Crackdown isn't even close to the greatness that is Garry's Mod, but for shear mindless, cathartic, free-form fun there's few games like it. It's not deep. It barely has any kind of narrative. What it does have, however, is hours of fun for anyone with half an imagination and the ability to make their own fun.
I was originally intending to post about Homeworld, but I figured enough people played and absolutely loved that game enough that it can't really be classified as "underrated".