1) Earthbound
2) Dragon Age: Origins or Paper Mario/TTYD, I'm not sure which I spent more time with.
3) Minecraft. Can't even describe the number of hours I sunk into that while furnaces were heat treating samples or the XRD/SEM/TEM were doing their thing, or while I was waiting for someone else to get off the machines so that I could get on. Weekdays Monday to Friday, three or four hours a day, at least, for what...8 months? The others are just sheer number of playthroughs.
Skyrim and Fallout 3 are following close behind with about 200 hours each.