I don't have enough self-control to limit myself to just one - just picking one boss from some individual games is hard enough. Some, but not all, of my favorites include -

Goht from Majora's Mask
The End from Metal Gear Solid 3: Snake Eater
Ultros from Final Fantasy VI
Mr./Lord Passion from Mother 3
Just about any of the colossi (although the 5th one, Avion, might be my slightest of favorites) from Shadow of the Colossus
Stallord from Twilight Princess
Titan Dweevil from Pikmin 2
Ameno-sagiri from Persona 4
Psycho Mantis from Metal Gear Solid/The Twin Snakes
Rawk Hawk from Paper Mario: The Thousand-Year Door
Feral tigers from Yakuza 2 (I don't think they even had names - I just know that fighting two full-grown tigers with my bare virtual hands and winning is one of the greatest things ever)

Watch out guys, he has knifes!

Gorea (Metroid Prime Hunters)
Metal Face (Xenoblade Chronicles)
Bowser (Super Mario Galaxy, Super Mario 3D Land)
Eox (Phantom Hourglass)
Colossus (Dementium II)
Captain Skull (Wario World)
Karate Kong (Donkey Kong Jungle Beat)
Egg Hammer Fortress (Sonic Rush)
Yin Yarn (Kirby's Epic Yarn)
...and much more

Almost forgot, this guy...

The first one that came to my mind was Melbu Frahma in The Legend of Dragoon. I'll link to somebody beating him: http://www.youtube.com/watch?v=k7qKbLlskyA It's a long boss fight with several phases. Oh, and how many games have final bosses that turn into a freaking space ship!?

I also really enjoyed fighting Girahim in The Legend of Zelda: Skyward Sword every time. I love bosses that actually test your skills and can't be beaten by mindlessly attacking. I actually really liked all the bosses in Skyward Sword.

I'm not sure if I'd call it a favourite of mine but the first boss of Mimana Iyar Chronicle really sticks out in my mind. Only because of my first time facing it. I'm like, "Oh hey, a giant crab! OH GOD IT'S KILLING ME!!!" that was probably the toughest boss in the game.

Oh! OOOOHHH! How could I forget about the final boss of 3D Dot Game Heroes?!?!?! Seriously, that was awesome! He was really easy but just watch it! http://www.youtube.com/watch?v=dsHg060q6bk

Lance (GSC)
Drawcia
The King of Evil
Yami (from Okami, but the fight in TvC)
Tabuu
Ridley
Zant
Twinrova
Dr. Letz Shake
Destroy Man
Nightmare (Metroid)
Kraid
Hades
Thanatos
Smogg Boss (chibi Robo PP)
Zero 2

Master Necky!

EDIT: Screw Master Necky, Mother Brain is the best!

EDIT 2: I love Ganondorf.

Who else?

Also always liked 02 from Kirby 64.

Mr. Freeze in Batman: Arkham City

Garland from Final Fantasy, or the Squeak Squad from Kirby. The latter mostly because of the music and its bada** SSB Brawl remix. I also like most of the Dracula's from Castlevania.

There's dark samus, but when she laughs like a man is kinda dumb... Wait theres Rundas! Yes! His ice powers are awesome! He could take out a space pirate army with his power! He was also an epic boss fight! So yeah, certainly Rundas.

How do I post a picture without stealing other websites' property?

psycho mantis
-> i was like 12 years old fighting him and it blew my mind!!!

the sorrow
->yeah i dont want to spoil this fight for you^^

photobucket.com is my site of choice. You have to regester to use it though.

I'd hardly call The Sorrow a boss fight. I loved the final Boss fight, especially when "Snake Eater" starts playing.

Dang, Swiket beat me to The Boss. Still, though: The Boss. The setting is perfect for spoilery reasons.

Also, GLaDOS is probably the best boss fight of any game, ever. Although a few from BIT.TRIP (Growth and Catharsis) come pretty close as well.

So many great bosses.

Hmm probaly the final boss in TTYD in Oot I would say the Fire Temple boss and
in MM I would say the Swam Area boss even though he is relatively easy.

In terms of amazement, this guy, the Titan Dweevil, (Pikmin 2). Let's just say I didn't have many Pikmin left when I first encountered this monstrous arachnorb...

In terms of terror, the Water Wraith! (Also Pikmin 2). About as scary a boss as you can find in the Pikmin games.

But when it comes to the funniest boss I've fought, I'd have to say Hewdraw from Kid Icarus: Uprising. The fact that they all bickered like ill-tempered triplets just made the whole fight hilarious!

Dr. Eggman is the ultimate villain by far, though Thanatos from Kid Icarus Uprising comes close.