Based purely on how often I still play them today: 1. Dark Souls (most hours logged in a single game ever) 2. Demon's Souls 3. Megaman Legends 4. The Legend of Zelda - A Link to the Past 5. Katamari Forever
Runners up would be Battlefield 2 (played that for a long period of time but I'm not going to touch it anymore) and Stalker (spent countless hours modding the hell out of that game but I won't touch it anymore).
Ninja Gaiden (Black/Sigma included) SMT: Digital Devil Saga (I'm going to clump these together; if I only had to choose one, 2) Warhammer 40k: Dawn of War (including expansions) Pokemon Silver/Gold Ape Escape
PSN: MasamuneMonkey "I'm the warrior of love and rage, Black Frost!"