It's difficult for me to think of games that haven't received the recognition they deserve, because I'm familiar with a lot of niche titles which all have very strong fandoms. In mainstream media, 90% of the games I play are never given any recognition at all, outside of an unjustly scathing review that clearly shows whoever wrote it either isn't interested in JRPGs or didn't bother playing the game past the first couple of minutes. Online, it's a different story. There are a couple, though:
Resonance of Fate is the biggest one that springs to mind for me; I have met maybe two or three people who have played it, even on forums dedicated to the discussion of RPGs. This is criminal. This is easily one of the PS3's better JRPGs; it has an innovative and unique battle system reminiscent of VP2's, an interesting approach to telling its story which kept me playing it, a fantastic steampunk setting you hardly ever get to see in JRPGs, and it has a cast with great chemistry. It's a very, very good game. It just had the misfortune of being released shortly after FFXIII, so naturally it was completely overlooked. Resonance of Fate is the very definition of an underrated title.
The Guided Fate Paradox is another one; it seems to be the one that most NIS fans missed. It occupies its own little space as a spiritual successor to Zettai Hero Project - another title hardly anyone has heard of or played - and, as a dungeon crawler, it's pretty immersive. The sequel was awful, the spiritual prequel was completely ignored, but it sits in the middle, completely unnoticed. It deserved far more recognition than it got.
Since the official forums were shut down, Baten Kaitos has become this, too. It's not surprising, since there has been nothing about a third game for years and the second game wasn't released outside of the US (and you have no idea how pissed I am about that) but it's not one that crops up very often, and at the time of its release it was largely ignored in favour of the likes of Tales of Symphonia and Skies of Arcadia Legends. It's one of the better JRPGs to hit the Gamecube in my opinion, and it is in dire need of SOMETHING to make it relevant again. A port, a remaster, a sequel; anything. Too few people have heard of it.
There are definitely a few non-JRPG examples, but my brain isn't working this morning. I'll get back to you on those.