I list just a few titles (sorted by category), based on my experience and personal taste; there are several others that I don't consider as good:
-Action-RPGs:
Blood of Bahamut
Chou Shoujuu Mecha MG
Irodzuki Tingle no Koi no Balloon Trip
Soma Bringer
-Turn-based RPGs:
Metal Max 2 Reloaded
Metal Max 3
Saga 2/3
Tales of Innocence
-Horror-Action3Ds:
Nanashi no Game 1/2
-3D Platforms:
Okaeri! Chibi-Robo! Happy Richie Oosouji
-Visual Novels:
Rosario to Vampire
Otometeki Koi Kakumei Love Revo!! DS
Tokimeki Memorial: Girl's Side series
Vampire Knight DS
Meitantei Conan & Kindaichi Shounen no Jikenbou: Meguri au Futari no Meitantei
PC Visual Novel Ports (through VNDS):
Kira Kira
Fate Stay Night
Tsuki Hime
Kagetsu Tohya
Never 17
Kanon
Saya no Uta