Difficult to call really, the most underrated games are probably ones nobody has heard of. Same goes for all under/overrated <thing> threads, you can never get away from the debates about how "that can't be underrated, because people think it's good" or "that can't be overrated, because it's amazing".
I'll go perhaps with some on the better known end of the spectrum:
-Freespace 2 - for some reason Freelancer gets more attention, but the combat, story and control mechanism are vastly superior in FS2. Maybe a bit of a stretch to call it underrated, but in comparison to Freelancer, definitely.
-Deus Ex: The Invisible War - got a bad rep because it was dumbed down and not as good as Deus Ex. I had the fortune to play this before I played Deus Ex, so I could judge it on merit, rather than constantly comparing it to one of the best games ever.
-Chaser - has a lot of flaws but it also has good combat, a developed storyline and lots of levels. Hardly anyone seems to know about it, some thing it's rubbish (which is why I have it as underrated) but as generic shooters go, it ticks the boxes
-Bulletstorm - doesn't take itself too seriously, I like the game mechanic that rewards fancy kills rather than just chasing arbitrary "achievements"
-Medal of Honour (2010) - brilliant set pieces, reminds me of a modern day CoD.
-Tribes Vengeance - for the 3d combat mechanics, some shooters have "flying sections" but they actually managed to base a whole game pretty much around jetpacks
-Homefront - quite short but a like squad shooters with AI teammates, it also builds quite an atmosphere. I don't think I'll ever forget the bus ride into the city at the start, the scene where a toddler witnesses his parents execution....
Almost made me sick,I'm surprised that didn't get banned. I've played games since the 80s and I'd say that's the single most harrowing scene I've seen in gaming, makes Spec Ops: The Line looks like Cbeebies.
Singularity I don't think is underrated per se - most people that comment on it seem to be positive. I'd say it's more a good game that never got much publicity.