Honestly, my favorite boss battle would have to be Oogie Boogie from Kingdom Hearts II.
Then again, the Jill boss battle in Resident Evil 5 set an intense atmosphere.
What’s yours?
From Kingdom Hearts 368/2 Days, I like the final Xion form. It’s so easy to play around with and break! :D
Even though I have NEVER played the game before, I’d have to pick…
Young Master Xehanort from Kingdom Hearts: Birth by Sleep. 
Almost ALL of his attacks can kill you INSTANTLY if you’re not prepared, the fight is memorable, it’s an OPTIONAL boss battle, and then…
…there’s the music, Dark Impetus.
…IT IS FREAKING AMAZING.
Overall, this is possibly one of, if not, THE best optional Kingdom Hearts boss battles ever.
Every boss from Tails Of Symphonia. :>
They are nearly all Kingdom Hearts bosses at the moment. Gotta love that.
My favourite would probably have to be…Koloktos from Legend of Zelda: Skyward Sword.
Gotta love the music and just the whole mechanics of the boss battle. Ripping off his arms and then attacking his core. Especially when you got to wield one of his swords. Epic. The music really sets you up for what is to come and fits this boss perfectly.
Yes I know, before you faint I haven’t mentioned a Kingdom Hearts boss, but eh what ya gonna do? I’m not completely obsessed with Kingdom Hearts people! Looks at avatar and signatures Oh dear…
Every boss from Persona 4 :)
You’re amazing. <3
Hmmm I liked the REAL final boss in cave story.
That or Primal Dialiga 2.0 (In the future of darkness version)
(P.S: Please don’t hate me for this, but am I the only person on this site who DOESN’T like kingdom of hearts!?)
Mine is pretty obvious.
Cackletta’s soul from Superstar Saga
<3
My favorite boss is from Kingdom Hearts 3D, so I don’t wanna spoil it, so i’ll put it in a spoiler.
It would have to be Young Master Xehanort, 
plus the song, L"Impeto Oscura is amazing.
The final boss battle in Okami against Yami was amazing. Especially the music that plays during Yami’s very last phase, though the theme before that is still very cool and demonic-sounding. 
Another big favourite would be Yuyuko Saigyouji in Perfect Cherry Blossom. Again, that final phase (or Last Spell in Yuyuko’s case)…the theme, the danmaku, it’s all so beautiful and yet deadly at the same time. 