Eternal Darkness for the Gamecube was very good, I think it was released around the same time as RE: 4 which is probably why it didn't do so well.
Jade Empire is one of my favorite RPGs ever, with very unique world (as far as western RPG's are concerned).
Dragons Dogma by no means an amazing game but it's combat is easily overlooked and it's one of the best I've seen in a hack and slash fantasy action game.
Darksiders I and II awesome series, in my opinion way better than God of War (and I loved 1-3).
Shin Megami Tensei series not so much underrated but unknown outside of Japan. Always enjoyed it more than Persona.
Way of the Samurai series and Yakuza series very funny games with an enormous amount of replay value.
Sleeping Dogs enjoyed it more than GTA 5 story wise.
Empire Earth 2 I don't know why but back when Red Alert 2 was all the rage I use to play EE 2 much more. Something about the map maker was just much more fun in that game.
Rogue Squadron series my most played game on the Gamecube after Smash and Zelda. This series needs to come back.