I doubt I'll get much agreement for either of these but...

Enter the Matrix: Alright it had some horrible platform and collision problems, but the hand to hand fighting was damn fun. It was simple, but you could make some very cool looking fight sequences. Plus, despite being horrifically under-developed (to the extent that a lot of people didn't even know it had one), the multiplayer could actually be a lot of fun. It isn't amazing, but it gets slated when there is actually quite a lot of fun to be had from it.

The Grand Theft Auto series... Yes I know, underrated is a stupid word to use generally, but among gamers it gets a hell of a lot of stick that it doesn't deserve. I don't know if its because its so popular, or because a lot of people who play it just cheat the hell out of it, but the 3D games were exceptional in terms of scale and variety of things to do. Sure there are flaws, and I can even see how the main story mode would get annoying, but at the end of the day the games repeatedly pushed the boundary of how much you could expect from a game. I don't like the games because they let you commit crimes and such (I'd have preferred to be a good guy), I like them because you can do so much, and so much of it is fun.