Hmmm.... fav boss would be Chernabog because 1. He was my favorite Fantasia piece as a child. 2. He was a challenging boss to the point where he could blast you to the back of the field so you had to fly back to him and his wings got in the way.
That being said, it's hard for me to choose between my actual two fav bosses because the second one is just as cool so I have to state him. Phantom. He's so awesome. Why? Beating him takes major skill and patience. It really puts you to the test where as the battle with Sephiroth was simply based on your ability to dodge and how many items you had. Though I worship the digital ground Sephiroth doesn't really walk on, he sucked in Kingdom Hearts. He looked like a vampirric Bat Man. The only things good about his design were his hair and his sword. You want to see Sephiroth in all his glory? Play Final Fantasy VII. If you have already, isn't the first disc just a b**ch? If you haven't, it costs 'bout 14 bucks at a good ol' K-Mart. Go and buy it, it's worth it. Beat the first disc in about, oh... 6 months? Beat the second disc in two days. Beat the third and final disc in two weeks tops.