So this was sort of something that I saw on blitz233 's book, and I thought it be a good idea to take that up to the next level. Instead of just Pokemon music, I would like to try to make a list of the 10 most characteristic/epic final encounter themes of games that I've personally played. Give these games a try if you do get the chance to, I recommend it^^
(I'm also limiting it to 1 per series- just because there's a LOT of good music in these series)

*There may be spoilers for a few things, so discretion is advised*

Without further adieu:

#10: Primal Dialga's Fight to the Finish: Pokemon Mystery Dungeon Explorers of T/D/S
https://m.youtube.com/watch?v=nxS8YDjTpeg

Now, I figured this would be pretty obvious for anyone who's known me for any length of time. Just a quick look at my profile makes it pretty obvious that I'm a PMD nerd, so I have a bit of bias.

What makes this 10 on the list, though, is that
1. Dialga's not actually the true final boss, only the finishing arc of the main campaign.
2. This theme, while nostalgic, isn't heard for very long because Dialga is a cakewalk and a half if you prepare.

I will give the music credit, though. The track, itself, is expertly metered and symphonic. This makes sense since we're, yknow, fighting the being that controls TIME. The two tracks playing together just make it that much more enjoyable.

Overall, though, due to its short length, it doesn't get to set it's mood as well. I think Temporal Tower does a better job of doing that since those dungeons are a slog and a half.

#9: Chairman Drek: Ratchet and Clank
(Or Gleeman Vox: Ratchet and Clank, Deadlocked)
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Here's where we start to divert from Pokemon quite a bit. Number nine on this list goes to a theme that might as well be the angry revamped version of the 1812 Overture. There's just so many instruments that crop up, but they all add to the growing building undertone of the drums and main harmony that it just makes me happy. And for those who have played the game, Chairman Drek is a huge dick to everyone, even going so far as to basically attempt to eradicate the planet of everyone that stood in his way. He needs to go- too bad this fight is also hilariously easy if you have any of the Gold Weapons or play the PAL version.

The same goes for Mr. Vox. After being trapped in the DreadZone battle station for the entire game, we finally get the chance to take on the guy that's been pulling the strings the whole game after carrying out our elaborate espionage plan. The music sets the tone just as well as Drek did- instead of defined, though, Vox is maniacal and erratic, which his theme definitely demonstrates. Ultimately, this falls short of being difficult, just like Drek did, though.

#8: Boss Cass's Robot- Ty the Tasmanian Tiger
https://m.youtube.com/watch?v=ReIgpR-zmlU

What can I say? While this loop is really short (like thirty seconds long total), it really sets up the final face-off with the massive mech that we got to watch demolish part of the Outback. And for all the crap you had to do to unlock this fight, there's nothing more satisfying than throwing a Doomerang down the exhaust pipe of Cass' robot and watching it spontaneously explode.
Did I mention that this game takes place in basically Australia? Because that's a plus, too.

#7: Specter Face-Off!: Ape Escape 3
https://m.youtube.com/watch?v=L0cMyZ2cxeY

Now for something a little different. I can't imagine anyone expecting this type of thing to be on the list, but my goodness, I can't get enough of this game for whatever reason. Just the concept is interesting enough, but the music adopts its own style and does it VERY well. Even the first two games, while I didn't enjoy them as much, still had pretty solid soundtracks. This takes it up to eleven with it's zany cast of characters and music that matches, heralded with the synthetic backbeat that makes up Specter's final fight theme.
Great game, great track but it suffers from the same "this is too easy" mentality that brings down the earlier entries on here.

#6: Neo Cortex: Crash Bandicoot 1
https://m.youtube.com/watch?v=38kIZt-KDG8

Another hidden gem from older games (can you tell I play a lot of those yet?). This one, while I do know that there is a remastered version of it, trumps that other version in practically every aspect. The track, itself, it so simple- yet it achieves the desired effect in spades. Here you are, fighting atop a blimp with the mad scientist that brought you into existence, while N. Sanity Island burns around you. In the original Crash games, Cortex was undoubtedly a madman, and this, combined with some of the earlier tracks (like the Generator Room) really sets that in stone. The atmosphere is just grandiose- my only gripe is that he's not hard to beat at all, regardless of the version you play on.

#5: A Strange Reunion- Sly Cooper and the Thevius Raccoonus

Another hidden gem, this theme certainly asserts the gravity of the situation where it plays. After an entire game's worth of reclaiming your own heritage- the namesake book of master thieving tactics- from the hilariously easy first four of the Fiendish Five, you're suddenly thrust into a gauntlet of platforming, shooting, and other such levels that actually require some know-how to get through. And where does this take place? Atop an active volcano in Russia!
By itself, some of them aren't all that hard, but in a full-game speedrun, those last few levels are killer. Especially since the last thing you did before the final boss reveals itself was climb a massive tower sinking into lava. Like that wasn't nerve-wrenching or anything.

After all that, though, the last enemy standing in your way attacks without warning- the massive reconstructed bird foreshadowed from the very beginning of the game, Clockwerk. Living off of literally nothing but hate as fuel, he's relentlessly trying to vanquish you and your ancestry.

The theme is just as hectic, sporting a mechanical "chanting" accompanied by an awesome synth track that just makes me smile, as it fits the hidden hate that's fostered in Clockwerk for all these years.

#4: The Dark Maker: Jak 3
https://m.youtube.com/watch?v=finKks9Qc1s

This where difficulty actually starts existing on this list, so I figured it best that it happens past halfway down.

I must say, though, the way this theme meshes with the atmosphere is just fantastic. After thwarting the operations of the nefarious Vegar, your next task is to investigate the disturbances in the outskirts of the Wasteland.

Oh yeah, and remember that guy you thought you killed earlier in the second game? Errol? Yea, he's back, and his vengeance knows no bounds. After falling into a pit of Dark Eco, his body was reconstructed- and his mind still harbored an intense grudge against Jak for this.
Harnessing the power of the Dark Makers, Errol attempts to destroy the world, until his ship is shot down by our defenses. Then, he descends to the ground in a massive terraformer and attempts to brutally crush all who stand in his way in one final charge.
Trust me, on Hero Mode with limited ammo, this guy is no joke.

#3: Paradise Lost: MegaMan X8

Another odd game? Let me preface this by saying that while I'm not a huge MegaMan fan, I have played this game since I randomly got it at a garage sale one day. Quite a good game, but my goodness, it's hilariously frustrating on the hardest difficulty (because what is playing on anything else tbh?). The soundtrack, overall, matches the environment, and it's all the better after your heart races from almost touching the many instant-death hazards of Sigma Palace, the supposed stronghold of the Reploid attempting to conquer the world- and it's located on the moon.

Finally, at the end of this absurd slalom of a level and a few other bosses, you come face-to-face with Sigma himself. One epic showdown later, and the game ends.

Or, at least, if you're playing on the Easy difficulty, it is. Otherwise, the operator of the Jakob Orbital elevator project, Lumine, teleports into the room to congratulate you... Seconds before he copies the data of Sigma and attacks you, exposing the fact that he was the one attempting to purge the world of everything that wasn't a new-age Reploid.
This fight definitely takes the cake as the most input-heavy on this list, as it requires quite a bit of knowledge about character movement to not end up getting fried by a laser.

Two phases of this later, you think you've won, until Lumine utters the immortal words "Paradise Lost" and you have about twenty seconds to finish him off before he instantly kills you and resets the boss fight. Good luck, you'll need it!

(I'll finish the last two in the next entry)

#2: The Shadow Queen's Resurrection: Paper Mario TTYD

#1: The Fate of Two Worlds: Okami