Including Japanese games, here are some that weren't mentioned so far:
- Bou Ningen Charengi (REALLY obscure game even during FreeShop's era but it's amazing, it's basically a compilation of minigames that each use a different function of the 3DS like gyro/touch/mic/etc. and tons of fun, just it's Japan-only)
- Neko Atsume Kitty Collector (let's be honest, this is just a nice game to relax with playing around with cute kittens
also Japan-only but it's also a mobile game and that version is in English)
- Labyrynth no Kanata (dungeon crawler, REALLY good, Japan-only but there's a 100% English Patch released for it so it's not a problem and the game has a lovely twist, so if you start playing don't think "graphics suck" and stop, keep going
and don't google it to avoid spoilers...)
- Sanrio Characters Picross (it's a picross game but with Sanrio characters so Hello Kitty and the like, but while not interested in the characters, as a picross game it's easily one of the best on the 3DS if not THE best, Japan-only again but hardly any text so not a problem)
- Zombie Panic DX (fun shooter game where enemies come at you and you can only shoot and strafe to avoid them, happens to be by far one of the hardest games on the 3DS yet it's incredibly fun)
- Samurai Defender (just a fun little tower defense game, nice way to relax or good pick if you just want to play something for 10-20 minutes every now and then)
I could suggest a LOT more, mainly Japanese since I've gone through literally all Japan-only games just to find the hidden gems, but can't find the spreadsheet I kept with them...