Stealing this idea from Reddit, as it's always pretty interesting to see what other people have spent the most time on their 3DS doing. I guess we could include Wii U here as well, but primarily this is 3DS oriented.
I'll start us off:
Steps 30,880
Animal Crossing New Leaf 26:23
Pokemon X 6:47
StreetPass Mii Plaza 5:02
Mario Kart 7 3:30
Disney Magical World 2:49
Kirby Triple Deluxe 1:11
I've been playing a lot of Ace Attorney. I finished up the DLC case of Dual Destinies just about a week ago, and I'm not waiting on my copy of the first one to come in so I can replay it.
Other than that, I've been playing Pokemon and occaaaaassionally stopping in to see my New Leaf town.
I also have really been meaning to play more of Chibi Robo: Photo Finder but I never seem to find the time to do more than walk around for five minutes.
I can't say how long I've played these (I would need to check my Activity Log, but my 3DS is recharging), but my top three would be:
1) Professor Layton vs. Phoenix Wright: Ace Attorney
2) Pok?mon X
3) Animal Crossing: New Leaf
My goal is to finish Professor Layton vs. Phoenix Wright: Ace Attorney (I'm 12 hours into the game) next week and after that, finally finish Pok?mon X (I can't keep playing for longer than 30 minutes; I just get bored so easily, blah).
Animal Crossing: New Leaf:3:29
Face Raiders: 0:09
Nintendo Network ID Settings:0:07
Friend List: 0:04
Nintendo 3DS Sound:0:03
Mii Maker: 0:02
Miiverse:0:02
System Settings:0:01
StreetPass Mii Plaza: 0:01