Oh god, where do I start?
NieR is easily one of the most beautiful and heartbreaking pieces of storytelling I have ever seen in a video game. It has a dark and gritty world with a very sinister sense of humour and, whilst it doesn't reveal very much until the very end, it's filled with twists, especially if you play it more than once. By the end of my second playthrough I was in awe of what it had put me through; I felt really, REALLY despicable for the role the game had thrust me into. We were lucky enough to get the Gestalt version instead of the Replicant version localized, which I think adds so much more depth to the protagonist; a father out to save his daughter is a lot more scarce than a sibling relationship. The cast outside of that is also fantastic and unique, and has a weird sort of chemistry that makes for a very entertaining tale...despite the gritty and constantly depressing atmosphere.
...it also has the greatest video game soundtrack in existence. That is perhaps the only thing about it that ISN'T underrated - a lot of well-deserved praise has gone towards the OST, but the game itself is constantly criticized by people who clearly didn't play beyond the first ten minutes. It has a spectacular story and cast that is well worth experiencing.
Resonance of Fate is another one that was released in the shadow of the vastly inferior and highly disappointing Final Fantasy XIII and received little to no praise or attention, despite its interesting Valkyrie Profile-esque battle system, absolutely brutal learning curve - I ragequit twice on this game for months because of it - steampunk premise, and vaguely religious story. The camaraderie between Vashyron, Zephyr and Leanne more than makes up for the occasionally slow moments. We don't get many steampunk JRPGs anymore, and this one is tragically overlooked.
I'd call ZHP: Unlosing Ranger vs. Darkdeath Evilman and its spiritual sequel, The Guided Fate Paradox, underrated as well...as in, hardly anyone has heard of them. Most people think only of Disgaea when they think of NIS, but these two games were pretty good, the former for its fantastic sense of humour and for being able to make an entire game based around a single boss battle - which you lose repeatedly - and the latter for being the most brutal dungeon-crawler I've ever experienced. I expect The Awakened Fate Ultimatum will suffer the same fate as these two when it's released...
Vanquish is another one...Platinum Games have been so successful with Bayonetta that this has been completely overlooked...and it's just as fast-paced and exciting. It's also a lot harder. It has a very generic look to it, admittedly, but it's a lot of fun to play.
Oh, add Baten Kaitos to that list as well. With the likes of Tales of Symphonia, Paper Mario 2 and Skies of Arcadia, it's easy to see how this one got overlooked, but it's a shame that it did - it boasts some of Sakuraba's finest compositions, a unique card battle system that actually WORKS for a change, and a fairly intriguing story.
