Exactly as it sounds.
Now, leaving aside the fact that my gaming diet hasn't consisted of much, I still came across a few gems.

My favorite is Dingodile's battle from Crash Bandicoot WARPED. A great soundtrack, a funny character, that penguin, and great battle
http://youtu.be/4LktWhQrPHI?t=8m57s

Other than that.. idk. Maybe bowser, but he's not one I actually go back to fight just because.

That's easy. The Dragon from Dragon Age Origins is the most epic RPG battle ever.

-the Arbiter's Ground boss in TP
-Goht from Majora's Mask
-final boss from OOT
-final boss from Yoshi's Island
-Metroid Prime from...er...Metroid Prime
-like at least half the boss battles in No More Heroes
-at least a few from No More Heroes 2
-all the major boss battles from Little King's Story
-all the major boss battles from the first 2 Paper Marios

bowser from new super mario bros wii/U
the final ship from ftl

these are all that is on the top of my head.

Captain Vladamir (NMH2)
Majora (Majora's Mask)
Final Ghirahim (SS)
Xord (Xenoblade Chronicles)
Final Boss of KIU
King K. Rool(DKC)
Nightmare(Kirby's Adventure)

Bowser (Super Mario Galaxy 2)
Titan Dweevil (Pikmin 2)
Wheatley (Portal 2)
Demise (Legend of Zelda: Skyward Sword)
Andross (Starfox 64)

This thread has been done before, but I'll share some of my many favorites anyway.
http://www.nintendolife.com/forums/general_discussion/what_is...

I forgot to mention this last time, but I really should have.

Mr. Freeze from Arkham City
Gaius from Shadow of the Colossus(but in all honesty all of them are awesome)
Leviathan from Dead Space
The great mighty Poo from Conker's bad fur day
If I we're to mention a boss from Metal gear series i'm going to say.....Laughing Octopus.

Favorite RPG boss Matador from SMT: Nocturne.

Not copying off on anyone above me here, but these I consider my favorites:

Bowser in Super Mario Bros.
Bowser in Super Mario Bros. 3
Bowser in Super Mario 64
King K. Rool in Donkey Kong Country
Kaptain K. Rool in Donkey Kong Country 2
Death Egg Robot in Sonic the Hedgehog 2 - This one is enough to get me frothing at the mouth; I like a challenge.
The Silver Sonic in Sonic 2 Game Gear
Baby Bowser in Yoshi's Island
Donkey Kong's robot in Mario vs. Donkey Kong
Bowser in Super Mario Galaxy
Bowser in Super Mario Galaxy 2
Bowser in New Super Mario Bros. Wii
Medusa in Kid Icarus
Medusa in Kid Icarus: Uprising
The Heart of Hades in Kid Icarus: Uprising (another one that can get me frothing at the mouth)
Hades himself
Bowser in Super Mario 3D Land
Baron K. Roolenstein in Donkey Kong Country 3
Tiki Tong in Donkey Kong Country Returns
Egg Viper in Sonic Adventure DX (never had a Dreamcast)
Egg Walker in Sonic Adventure DX
Perfect Chaos in Sonic Adventure DX
The Biolizard in Sonic Adventure 2 Battle
The Finalhazard in Sonic Adventure 2 Battle
Metal Madness/Metal Overlord in Sonic Heroes (about the best thing I like about the game)
Sonic & Diablon in Shadow the Hedgehog
Devil Doom in Shadow the Hedgehog
Solaris in Sonic '06 (yes, I actually like this game)
Dark Gaia Phoenix in Sonic Unleashed
Egg Lancer in Sonic Unleashed
Dark Guardian in Sonic Unleashed
Egg Dragoon in Sonic Unleashed
Dark Gaia/Perfect Dark Gaia in Sonic Unleashed
The Dark Queen in Sonic and the Black Knight
Lancelot Returns in Sonic and the Black Knight
Sir Percival in Sonic and the Black Knight
Frigate Skullian in Sonic Colors
Egg Nega Wisp in Sonic Colors
E.G.G. Station Zone in Sonic 4 Episode 1
Dr. Eggman's Conveyor Belt in Sonic CD
Metal Sonic in Sonic CD
Big Arm in Sonic the Hedgehog 3
The Giant Eggman Robot in Sonic & Knuckles
Knuckles in Sonic & Knuckles
The Doomsday Zone in Sonic & Knuckles
Metal Sonic in Sonic Generations
Shadow the Hedgehog in Sonic Generations
Perfect Chaos in Sonic Generations
Silver the Hedgehog in Sonic Generations (much more fair than the fight against him in '06)
The Omega Metroid in Metroid Fusion
Metal Sonic Strikes in Sonic 4 Episode 2
Metal Sonic in the Death Egg Zone mk. II in Sonic 4 Episode 2

I know this list is pretty haphazard, but I do like these bosses.

• SMW Bowser (mainly nostalgia as the first final boss I've ever beat)
• TP Ganon
• KH Sephiroth
• Nightmare (Link's Awakening)
• Nightmare (Kirby's Adventure/Nightmare in Dreamland)
• The Sorrow
• The End
• KH Ansem
• KH: DDD Ansem
• KH Xemnas
• Volvagia
• Twinrova
• Stallord
• Kurt Ziza (probably misspelled that)
• That optional phantom boss in KH

Probably many more that I can't think of, lol.

Another one, he's always been a favorite since I was a kid. Ripper Roo from Crash Bandicoot series. Not much of a challenge anymore lol
As for a specific bowser battle. I don't know. He's just, well, bowser. It's not really about the battle, though SMW was the best.

It has to be Gannon in Ocarina of Time as it complimented the story perfectly.

Gray Fox

The frog from Yoshi's Island
Bowser in 3D Land
Bosses with music/ rhythm involved in fighting (like the Pinchin' Pirates from DKCR or Gooper Blooper in PM:SS)
And i like fighting Eyerok (SM64DS) as Yoshi, even though i'm not that sure it's possible to actually hurt him. But it''s also hard to get to him because you're supposed to be one of the humans to get in.

Mr. Freeze in Arham City.
Seriously, no other boss fight ever even comes close to the epic awesomeness there.

Number 1 rule when discussing Metal Gear: Don't post spoilers.

Egg Robo from Doomsday Zone in Sonic and Knuckles and for some reason I really liked the last Bowser battle in World 8 from Super Mario 3D Land.
Edit: I also loved the last battle against King K. Rool in DKC, Baby Bowser in Yoshi's Island and The Shadow Queen from Paper Mario: The Thousand Year Door.

Someone else on here actually likes Crash Bandicoot! Yeah!
I can only think of a few right now.

• Scorch from Spyro: Year of The Dragon - As a child, he was literally nightmare fuel for me. He lives in the skeleton of a dead beast, the dungeon you fight him in, and he's a mutated version of a regular enemy. To some extent I'm still scared of him. It's really his home that does it for me and it's probably the scariest location in concept and design I've encountered in a video game, just because of my nostalgia with it.
• Medusa from Kid Icarus: Uprising - I love seeing a serious final boss with a personality like this and I honestly wish Hades hadn't usurped her so much. She should have stayed in the game for longer and I wish she had been the final fight at the very end because as much as I like Hades Medusa is simply much more awesome. She's Palutena's sister driven by jealousy, she's simply an old trope... Done fantastically.
• Fawful from the Mario & Luigi series: I HAVE FURY!