1. Civilization II or IV
I'm not sure which game I've played more, but both have taken weeks from me. I've only gotten about a hundred hours into Civ 5, so Civ 1 probably takes the third spot. Trailing behind is Civ 3, which I never really played all that much.
2. Baldur's Gate 2: Shadows of Amn
I've played through the Big Picture modpack (BG + BG:TotSC + BG2:SoA + BG2:ToB + major mods) twice and several individual runs of both BG games with various mods, but BG2 takes the throne as the single game from the series I've spent most hours playing.
3. The Longest Journey
Well probably not, but I've finished it so many times it's bound to be pretty near the top. The actual third spot probably belongs to one of the lengthy moddable timesinks with high replay value, like Arcanum, Fallout 2, Knights of the Old Republic, Vampire: The Masquerade, Wizardry 8 or any other I fail to remember right now. Still TLJ is awesome and gets preferential treatment.