I really have to take a blind guess because, um, the games that I would assume would be the ones I played most really didn't keep track of play time. I suppose I can give you estimates but, they're probably nowhere near right.
Animal Crossing: Wild World (~800+)
Super Smash Bros. Brawl (~500+)
Mario Kart DS (~400)
Rune Factory Frontier (~400)
Harvest Moon DS (~300)
I was also really obsessed with Guitar Hero at some point, so I'm almost certain Guitar Hero III probably makes this list somewhere. To save myself too much embarrassment, I'll just slip it in as ~200 hours.
For stuff that's legitimately and accurately quantified:
My 3DS play log says my top 3 are: Animal Crossing: New Leaf (683 hrs), Fire Emblem Awakening (316 hrs), Rune Factory 4 (215 hrs). However, I shared New Leaf with my sister and allowed her to play it on my system, so, for me, that probably isn't 100% accurate.
I don't think any of my Wii U games have clocked over 100 hours (except Mario Kart 8 and maybe Smash 4), because I really don't play it much. I'm too lazy to check.