Okay, the idea here is to champion games you like that seldom come up in discussion and that many people may not have considered purchasing or might not even know about. So, it's not about underrated games. It's about games that, well, aren't often "rated" to begin with.
Here are some of my picks:
Bazaru de GozaruGranted, one reason it isn't mentioned all that much is that it's extremely hard to find. But it's a super-fun trial-and-error puzzle game with an amusing main character, and I think some people here (mainly Steve and Keranu) would really get a kick out of it.
Tenshi no UtaWell, on a system with so many brilliant RPGs, it's easy to get overlooked. This is one of the best, though, with fast gameplay, well-designed dungeons, and an excellent soundtrack.
Kiaidan 00A must if you liked any sort of "giant robot" show when you were a kid. Very cool stage concepts and enemy designs, and lots of enormous mecha to fight.
Private Eye DolA cool combination of digital comic and RPG elements. It's mystery solving with lots of wacky characters and some fun puzzles to figure out. Plenty of humor, but plenty of shocking moments as well.
Efera & JilioraDark action-RPG with cool music. Like an Ys with sword swinging. In fact, Mr Fulci rates it higher than Ys! (Note: Never mind that Mr Fulci isn't a big Ys fan.)
Sotsugyou Shashin * MikiTwo digital comics on one disc. To be honest, the Miki part sucks, but Sotsugyou Shashin is an endearingly corny love story with some very nice music.
Asuka 120%It's amazing that the mediocre Advanced V.G. is mentioned fairly often and actually receives occasional praise, while this FAR superior girl fighter receives little attention. Very fast, very enjoyable game.