I've only got a few. Several of them don't really track hours, but I know I've put over 1000 into them. Games like Super Smash Bros. (Melee, Brawl, and 4) and Rock Band 2.
Other than those, the only one I've measurably put 1000 hours into is Skullgirls, but Guilty Gear Strive will likely get there in a few years. Skullgirls is a game with so much depth that I can't imagine ever getting bored of it. If anything, I'd just lose motivation because I can't see the path to improving, but I'll definitely never see every permutation of strategies you can employ by combining characters together. Guilty Gear Strive has so many creative ways to use its expanded Roman Cancel system that any Evo highlight reel is full of creative ways out of situations that you've never seen before.