Most I can think of have already been stated, but Beyond Good & Evil is another definite underrated game for me. I know a few people online that feel it was great, but few IRL have even given it a go.

Knowledge of it in general isn't the best and that, combined with an excellent cast, story, look and varied gameplay - 3D platforming, stealth, photo taking, hovercraft events etc really make me feel it was one of the most underrated games of all time.