While this isn't the most memborable Sonic boss fight, the final boss of Sonic Adventure 2 is certainly one of the most epic, and the closest Sega has come to making a 3D Doomsday Zone. Right before you fight the Final Hazard, the seemingly evil Shadow the Hedgehog turns good and teams up with Sonic (and takes on a Super form along with Sonic) to fight a dinosaur-like creature that awkwardly fused itself to the cannon of a Death Star rip-off space colony that looks like Dr. Robotnik's face in order to bring the space colony on a collision course with Earth; all with the game's rockin' theme song "Live and Learn" playing during the boss battle.
Just for kicks: