Spoilers will obviously be present in this thread.
So, SPOILER ALERT:
Super Mario 3D Land's final Bowser battle is definitely one of my favorites. The section before the battle with the rain and no music is great. Following that, the battle itself is epic, having to run up the falling platforms. The music fits really well, too.
Both forms of the final boss from Megaman Zero 3. An epic "falling down" battle followed by an intense battle verus Zero's original form, Omega. It was that final blow that you can deal at the end of the fight that lead up to the biggest "HELL YEA" moument of my life.
Painful to pick one, Neo Exdeath from Final Fantasy V. All I through VI's original bosses exuded some level of horrific fascination, and for their time were as visually scary as they were challenging. Unforgettable elemental battles accompanied by haunting music.
I played through A Link to the Past recently, and the battle with Ganon was designed really well. It was challenging, but it was enjoyable. It didn't seem tedious like other bosses, even though it took a few tries to beat. It was actually fun.
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