Well, 3DS is really on fire. Not only HW-wise, but also software-wise.
Dragon Quest VII 827.922
Very solid debut
Animal Crossing: New Leaf 81.559 / 2.513.424
Unstoppable
Fantasy Life 13.342 / 221.720 (-35%)
Solved the stock issues, is still performing well. Very solid debut for a new IP from L5, that could still count on its "evergreen" franchises and finally was able to found another "Ninokuni" kind of game to be exploited (Nino was huge on the DS but I think that this one will still sell for awhile and could be better managed in terms of franchise)
New Super Mario Bros. 2 11.685 / 1.910.708
Not as hot as on DS but still performing very well. 2 millions is near
Monster Hunter 3 Ultimate (Best Price!) 10.523 / 218.097
As said in the other thread, it's performing really well and adding the LTD of the normal edition could hit 2 millions. Not bad at all.
Taiko no Tatsujin: Chibi Dragon to Fushigi na Orb 7.459 / 416.033
When we talk about long seller, here it is one of them. Strong LTD up to now and not fading at all.
Tousouchuu: Shijou Saikyou no Hunter-Tachi Kara Nigekire! 7.383 / 420.815
This is some of those unpredictable successes that was so popular on the DS
Paper Mario: Sticker Star - 6.452 / 518.096
Best episode ever in the series and still selling
Inazuma Eleven Go 2: Chrono Stone - Neppuu / Raimei 6.121 / 414.207
Here we are with the stable L5 brands as I think Prof Layton will be also with the 6th episode, considering the solid result of the spinoff.
Mario Kart 7 5.674 / 1.972.440
As for Mario2, not at DS levels but very solid. Also here, 2 millions is near.