Off the top of my head, there's Game Center CX 3, EX Troopers (I mean, there's the PS3 version too, but the 3DS version actually runs better for some weird reason), and physical versions of games that are digital only elsewhere like Ace Attorney Trilogy (You can switch between the JP and US versions of the game at the main menu, effectively giving you a english language physical release), and Sega 3D Archives (Apparently, this one doesn't work through RegionThree; You have to have a JP 3DS to run this)
Someone could probably think of a few more, but those are the must haves I can think of that don't require much Japanese knowledge.