My Activity Log is a bit inflated because I share the 3DS and games with my brother and we both play a lot. These are my top five most played:
Animal Crossing 1128:30 (1019 times)
Bravely Default 281:00 (206)
Shin Megami Tensei IV 250:17 (193)
Fire Emblem Awakening 182:22 (137)
Kid Icarus Uprising 95:30 (132)
No surprises there, I guess. These are all very long, time consuming games and we both like to complete games as much as we can. The time should be about equally split between the two of us, but he usually takes a bit longer than I do. Aside from these, the StreetPass Mii Plaza has been played for 310 hours and 1245 times (whoa...)
The 3DS's Activity Log is great, I like checking it regularly. It's such a shame the Wii U's Daily Log is so lackluster in comparison.
Fantasy Life™ 128:37 (Number 1 in average time played of 16:04! Only played 8 times!)
Holy crap! Haha. At one point I also used to just let the 3DS sleeping between Animal Crossing sessions. I know I'd probably sink as much time into Fantasy Life if I could play it.