Personally mine has always been a tie between Star Ocean:The Second Story, and Legend of Dragoon. Star Ocean may take it since I had two playthroughs on it and I had two different groups of allies and some different cutscenes. Plus the half active battle and traditional JRPG style battle mechanics. Legend of Dragoon just had some really fun mechanics with the additions. So instead of just sitting there and mashing 'X' to attack you instead have to learn these combos to do the most damage.
These are mine I am wondering what other peoples are, and please don't hate just because people don't love the game that you do. Since most people I talk to have never heard of my favourite.