I've had the most laughs with FFVII. The Turks (especially in Wutai sidequest), Cid, Palmer, "Kya Ha Ha and Gya Ha Ha", Don Corneo, the crossdressing scene etc were just hilarious. FFIX was also quite funny with all that goofy humor. A special mention to FFV too: the GBA-based script really fleshes out the dialogue, and especially Galuf and Gilgamesh are really funny.