Well the 3ds has been around for quite some time now, so I think it's safe to say we can make a top 10 list. Everyone nominate your favorites and let's get this thing started!
My nominations are Monster Hunter 4 Ultimate, Fire Emblem Awakening *shot*, bravely second, smash 4, Stella glow(I would place this over Awakening tbh), fantasy life, ocarina of time(does this count?), etrian Odyssey 2 Untold(also my nomination for best jrpg on the 3ds actually), Ace attorney dual destinies, shin megami tensei 4.
This is by no means in order, just my nominations. I would put mh4 at the top because of how much mileage I got out of it, and the really pretty good online multi-player(in most cases) with fantasy life being #10. The middle parts are a bit fuzzy though, a lot of them are super close.
Edit: there's gonna be a poll once we have a few submissions as to which games make the list, and after that i suppose a discussion should happen as to what order they place in. i'm looking forward to that part the most myself >.>