To me a truly great final boss has to have the following qualities:
- Epic location. Quite what defines epic depends on the style of the game, but it has to be something jaw dropping in scope in my opinion. IE: Planet's Core from FF7, the ruins of Ganondorf's Castle in Ocarina of Time, etc.
- Music that gets your blood pumping. The prime example of this in my mind is either One Winged Angel or Summoned Beast Battle from the Final Fantasy series. It has to be grand, dramatic, exciting and generally works better if it's orchestral music as it gives a better sense of scale, if you ask me.
- Personal reasons. It's not enough to just save the world, final boss battles work SO much better when it's against someone or something you just can't wait to face with your ready-to-open can of whupass. A bad example of this, where it somehow went wrong, was Final Fantasy 9. The final battle against Trance Kuja, that's fine. Suitable location, good music, long awaited beatdown. But then Necron appears pretty much out of nowhere (was he even mentioned before that?) and all of a sudden you're facing something you don't really care about. Personally I'd have had it as Kuja in his normal form, then Necron as an Eidolon he calls when things are going tits up, then his Trance form as the final battle. Would've worked much better.
- Difficulty. These battles are the culmination of your entire efforts for the entire game. They HAVE to give you at least some challenge, unless you've gone the extra mile for all the extra stupidly overpowered stuff that's near impossible to get your hands on, like Knights of the Round. Yu Yevon will always stick in my mind as the ultimate anti-climax of a final boss. The battle against the Aeons with that kick-ass music is unbelievable, filling all my criteria, then this tiny little purple blob shows up in a battle you can't possibly lose unless you deliberatly inflict Petrify on all your characters, which you have to do to yourself as he can't do it. What a let-down. At least the ending mostly made up for it.
Truth be told the one that comes straight to mind when I think of boss battles that fill all these criteria is the battle against Ganondorf/Beast Ganon at the end of Ocarina of Time. Fighting in the crumbled ruins of his dark castle as he launches one last-ditch attempt to take you down with everything he can muster, surrounded by walls of flame, your trusty Master Sword just out of reach, Zelda screaming if you take a hit, dramatic music playing overhead, a decent challenge (until you figure out Light Arrows are unnecesary as you can roll through his legs if you time it right, or if you went the extra mile to get the Biggoron's Sword), and the definitive battle against one of the greatest villains in gaming. A truly phenominal experience that even after over a decade still feels fresh and exciting. I eagerly await the 3DS rerelease to see how it feels.