Metal Slug is under represented. When was the last time you saw a Metal Slug cabinet in an arcade? I saw one, around 7 years ago and it was the only one I've seen. This series is pure 'run n gun' action at its best. People have heard of it, but no one's played it (except for maybe Metal Slug 3 because It's available now on the XBL marketplace and PSN store) but it's never mentioned, reviewers never allude to it, it's like a ghost.
Nascar Rumble and its sequel Rumble Racing are both incredibly fun racing games that no one played.
I think Street Fighter 3 has been somewhat neglected. It's been lost in the constant wave of praise fanboys throw at Street Fighter 2 and the people's love fest with the Alpha series and it's just been sitting there, getting played by some tournament players but ignored by the rest of the public. Hell, even Capcom denies its existence. There hasn't been a Street Fighter 3 character in any crossover game (Except Capcom Fighting evolution) until now that Capcom recognized it as its own and included 3 characters from it in Super Street Fighter IV, while the Alpha series has 7 characters in this installment.
Astro boy: Omega Factor was an incredibly fun GBA game. I don't know if it's underrated, but no one I know has heard of it and people didn't take it seriously because it was a licensed game.
There are more, just none that I can think of right now.
Oh, and Just Cause 2 deserved a 9/10 and not a crummy 8/10. IGN gave the Halo series high 9's every time when they didn't deserve it. Then they call themselves game critics.