I have 4 favorite boss battles

1. Sephiroth battle (Kingdom Hearts)

2. Battle with Riku at Hollow Bastion (Kingdom Hearts)

3. Ganon (Zelda: Ocarina of Time)

4. Grunty Battle (Banjo & Kazooie) - I know it sounds kinda funny but that was a fun battle, flying around on Kazooie trying to beak bust her ass. It also had a catchy tune!