Ganon--The classic
Mithos/Yggdrasil from Tales of Symphonia was also a sweet boss. He had a great and mysterious past and had those two sides to him that made him an enemy worthwhile to kill.
I have to agree wholeheartedly on that statement. Mithos was indeed a lovely VG boss. His first battle was naturally better, he's too damn easy to beat in that machine. Even on Mania Mode.
Anyway, my personal favorite remains Andross from Starwing.