Overall, I'm pretty sure it's Ninjatown: Trees of Doom. I remember clocking in something like 12 Hours on the in game clock.
Overall, I'd say either Phoenix Wright: Ace Attorney or Tony Hawk's Pro Skater 2. I've poured at least 20 hours into Tony Hawk... so actually, let's just go with that In terms of most recently: Probably Quell. I've been slowing down my iPhone gaming a lot lately, but what I have been playing is that one game, and I've put about 5 hours into it during the past week.
Overall, I'd say without a doubt it's Rogue Touch, with Battle for Wesnoth 2nd. At present, I'm playing a ton of Hexalex and Doom Classic. I've also recently gone back to HR Battle 3D and that's probably what I'm most consistently hitting, although Crimson Gem Saga, The Quest, and Pac-Man Championship Edition are finding heavy rotation as well.