Star Ocean 3 was right up in there. Forever a top for me. I have a bunch of games that have been near perfect, SO3 bein' the best. Tales of Vesperia, Persona 3 were up in there too. I'm just waiting for the one thing that will cease my undying love for SO3.
R-Type Delta is my perfect game. The ships, the difficulty, the challenge - all of it combined for a perfect degree of fairness, and it was always fun. Absolutely perfect. No other 2D shoot em up reached this level until I played Under Defeat HD in 2012... and funnily enough, that's an HD port of a seven year old Dreamcast game.
Your name is sung and tattooed now on my heart - here I will carry you forever CarryTori Amos