Final Fantasy VII
Final Fantasy VII is confusing as hell.
That's part of its charm; you spend most of the game just trying to figure out what exactly the hell is going on, and just when you think you've teased most of it out, the game laughs at you and says, "ha ha! WRONG again, bucko!"
Anyway, for all you hear this stuff about Sephiroth is the baddest bad guy that ever walked the bit-field, Sephiroth was just certified batshit insane. Even Kefka was the textbook diagram of sound mental stability compared to him. The real sinister evil you're struggling against in Final Fantasy VII is Jenova, the mastermind alien lifeform that crashed into the FF7 world (I think it's mostly called "The Planet" or "Gaia" in-game) a long time ago and has been plotting to eat out its soul since.
(If you're thinking, "it sounds a lot like Square's plotters said, hey, Kefka and Lavos were both crazy popular, so let's PUT THEM TOGETHER!", you are exactly right. And it worked exactly as they hoped. Sephiroth/Jenova remains the most popular video game villain in history.)
There's little to say about Jenova's boss battle theme except it's awesome, the high-pitched background beat is iconic, and yes, it can be done in an 8-bit version that is equally awesome. This is Final Fantasy VII's Super Boss music; actually, almost all of FFVII's Super Bosses are Jenova. Every time you think you're finally about to throw down with Sephiroth, sure enough, you hear those opening notes of J-E-N-O-V-A and here we go again with Jenova instead. You get used to it after a while. And maybe you even pick up the somewhat-subtle hint that what you think is Sephiroth you're chasing all over the planet is actually more like Jenova manifesting itself as him, or through him.