Yeah, I'm not doing this. I see what you're doing Spino, trying to make me waste hours searching for all those boss songs that I love until, once I'm done, I realize it's Christmas.
So, instead, I'll post 5 of my favorites. They won't necessarily be my 5 top favorites, but they are definitely among my top picks. And, on that note, only one per series. Also, sorry in advance for the descriptions, I'm not the best at explaining why I like songs and picking them apart to explain the meats (which shows a lot in my reviews).
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Persona 4 - The Fog
This theme is often overshadowed by pretty much any other boss or battle theme in Persona 4, and this is because it's only played once, and it plays for probably the shortest time of any of the other songs in the game. Heck, even I forgot it existed until I heard it as the Instant Kill theme in Persona 4 Arena. It's a shame, too, because this song is pretty powerful and really does well to keep you on the edge of your seat for the final battle.
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Phantom Brave - R&R Junkie
Phantom Brave has a great soundtrack, pretty much all of its songs are earworms to some extent, but if I had to choose my favorite boss theme from the game, it would probably be R&R Junkie, the theme of the boisterous Chroma Hunter, Walnut. I love everything about this theme, one part somber, all parts Western, this song is the perfect reflection of the character it accompanies, and I love it to death.
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Touhou 7: Perfect Cherry Blossom - Necrofantasia
If this were a list of my definite top favorites, this song wouldn't be on here. It couldn't be on here. There are FAR too many Touhou songs that I would have to wade through, make pros and cons lists of, create polls for, and do in-depth analyses of to get the correct answer for what my favorite it, because Touhou music is too good to just choose from. In fact, you know what, better idea.
Touhou
That list right there? Yeah, that's a mostly accurate.
...Though, on second thought, Necrofantasia is one of my favorite Touhou songs. When I think of the best boss theme, Necrofantasia definitely comes to mind. It may not be my favorite, but it's definitely up there.
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Final Fantasy XIII - Saber's Edge
Say what you will about Final Fantasy XIII, but it had great music. Though XIII isn't the first FF game to use orchestrals throughout the entirety of its soundtrack, it certainly is the one that utilizes them to their fullest, and I think this song is a pretty good indicator of that.
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Chrono Trigger - Battle with Magus
With an ominous lead in that quickly translates into a fast-paced theme, this is the battle theme when fighting Magus, the one who is surely behind all that happens in Chrono Trigger. Obviously back then, games didn't have orchestral renditions and such, and while this song doesn't use the most instruments, this one always felt the closest to that. Despite being relatively simple, it's a multifaceted song. Even though it's fast-paced and sinister, it still devotes itself to complimenting the dark setting that the battle takes place in, with distant laughter and that ever so chilling intro. At the same time, it feels pretty grand, like it deserves more than what could have been given at the time in terms of musical capabilities were concerned. It's a grand song that really does well to compliment the magnitude of the battle, as well as Magus himself.
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On a mostly unrelated note, to those of you that read this, I would really recommend posting links like Spino and Alfieri did rather than the posting the videos themselves. Reason being, the videos make the page take longer to load, and as more posts come in the longer it'll take. I've seen threads like this take up to a minute to load in their entirety because of direct video posts.