Perhaps not so much underrated (given its flaws) as underappreciated for just how much it illustrated the many ways in which "interactive narrative" can be done besides superficial dialogue/story trees and QTEs: Silent Hill Shattered Memories. Many will dislike it, but everyone, and I mean everyone, should play it.
Underappreciated and largely ignored because of a genre it brilliantly defies, vastly underrated because of its length which in my book should never, ever enter into the rating to begin with. I had so hoped that more people would let themselves experience it with the PSN release, but that didn't happen, so that's kind of a tragedy: Dead Space Extraction.
A different kind of underrated: Faulty review copies whose damage was never really undone ensures that we will never know how well Lost Odyssey might have scored.