I would say either Level-5, Armor Project or VanillaWare.
Level-5 of course has done a ton. Professor Layton, Inazuma Eleven, Dragon Quest IX, White Knight Chronicles. And now they've teamed up with Ghibli Animation Studios and are making both a PS3 and DS RPG set i nthe world of Miyazaki. If that wasn't enough, they've already announced 4 3DS games.
VanillaWare may not have the quantity of games of other compaies, but no one can argue their quality isn't through the roof. For a small independant game studio whose games only sell about 200,000-400,000 each, they have made some of the best games this gen. Including Muramasa: The Demon Blade for Wii and an upcoming PSP RPG.
Armor Project focuses completely on one series: Dragon Quest. But in just this gen, they have overseen the development of 10 different Dragon Quest games, with every single title improving on its predecessors with new features, updated graphics and some of the best innovation in the series to date.
Six upcoming games you should look into:
