Zelda: Spirit Tracks is the most underrated game I know that I like.
Okami is underrated too nowadays, because it barely sold and capcom had to close because of that - it's my fav non-zelda game. Okami is again way too underrated but not as underrated as ST.
I could write volumes on this topic.... so many underrated games getting NO LOVE that deserve it boy.... but for now I'm just gonna say the reviews and information circulating about Agarest War 2 that came out recently is completely ludicrous. I have read reviews (on reputable game sites no less) by which the authors CLEARLY did not play the game and based their "review" (if you could call them that) on the fact that it was a compile hearts/IF title with fan-service-ee stigma attached to it.
That game is freakin' great. Fan service is negligible (certainly MUCH WORSE going on with other JRPG franchises ATM), best soundtrack I've heard in ages and, as a complete departure from the first 2 agarest titles, the narrative is great and the battle system is completely different (battles go much quicker and are very much alike to that of valkyrie profile).