In the Game Boy Advance game Golden Sun: The Lost Age there were a few optional bosses that had interesting abilities. One was immune to Psynergy (basically magic) which made several strategies useless, but he was still rather easy to defeat. Another could use Djinn Summon spells (your most powerful attacks) against you which made preparing for those summons useless because he would use them first, but he was not to difficult either.
This last boss is arguably the hardest boss in the game. the star magician. It has a large amount of hit points, can use powerful spells, and can summon allies called balls. It can have four on the field at a time, and they come in four types. Anger Balls, which use normal attacks, weak magic, and a powerful self-destruct attack; Guardian Balls, which cast a protective aura which reduces all damage done that round to 10% (frustrating when a 1000 damage attack only does 100 damage and you won't be able to use it again for 4 or 5 turns); Thunder Balls, which attack with medium strength electric attacks; and Recovery balls, which can restore 1000 hit points (no easy feat to deal that much damage) to the Star Magician. You basically had to balance out to whom and how you inflicted damage. Sometimes it was more beneficial to allow the Thunder Balls to live because they took up a slot that could be filled with a more obnoxious ball.