There're a lot of bosses I've loved fighting from various video games. I'll list a few now and add some more as they come to me.
--Nine-Tails from Okami. I saw a video of part of this fight on GameSpot before I bought the game, and spent most of my time playing anticipating it. Needless to say, I was not disappointed; the musical score for the battle was great, and the whole thing was just damn fun. Honorable Mentions: Oki, Tei (rematch), and the Nachku/Lechku fights.
--Dark Chloe from Tales of Legendia. I enjoyed lots of fights in ToL, but my bias towards this fight comes from the overall difficulty. It's easily one of the most difficult battles in the game even on the Normal difficulty setting, and on Hard, I'd say she surpasses the final boss of the main quest (the game's first half, basically). Without proper preparation, she can rip your party to shreds with a single combo--I should know, since it happened to me. Honorable Mentions: Nerifes, Chloe, Dark Senel/Dark Shirley, Schwartz.
--Bill and Ben from Seiken Densetsu 3. You fight this pair twice throughout the game, and I'm counting both fights here. What really sold it to me here was the music; the track that plays for both fights really grants a frantic atmosphere, which I feel nicely complements the already fairly quick pace of the fights. Honorable Mentions: Dangaard, Zable Fahr, Bigieu, Archfiend.