Updated list, still in alphabetical order:
999: Nine Hours, Nine Persons, Nine Doors (DS)
Captain Toad: Treasure Tracker (WiiU)
Danganronpa: Trigger Happy Havoc (Vita)
Magician's Quest: Mysterious Times (DS)
Muramasa Rebirth (Vita)
New Little King's Story (Vita)
Poképark 2: Wonders Beyond (Wii)
Pokémon Mini system
Mainly these are either games that I've been wanting for forever, or that I can't seem to find anywhere.