It was a tough choice for me between FFX, KH2 and MGS3. KH2 won however. I only came to recently appreciate the MGS series over the last year, so despite how incredible an experience MGS3 was, to me it was inferior to the other 2 (I can completely understand if anyone disagrees with me). FFX only lost out, because it was only within the last 6 months that I felt the urge to purchase a copy for myself (which I did), after having completed it 4 times over, using an emulator or friend's copy. KH2 gets the prize however, since due to the strange, yet wonderful, and extremely successful combination of two favorite franchises, along with a great story, it seems to be a game, and also, game franchise I continuously return to (KH was not up in the top 3 as KH2 was superior for me)
RIP PS2. Here's hoping PS "Orbis" isn't a joke