Hard to keep it at one, and I've played so many games that I'm sure to have forgotten a few good ones, but those come to mind ...

The End in MGS3 blew my mind the first few times. Once you figure out his tricks he's really easy, but that didn't stop it from being fun, especially on Extreme.

The twins, Pollux and Castor, from God of War Ascension was an amazing fight imo. I love how it was sequenced and it kept me on my toes.

GOW: A again when I had to fight the Furies. Very memorable stuff with them, especially the last fight and the scenes leading up to it on the ship.

Shinobi on PS2. The fight with the moth boss over a lava pool while trying to kill her spawn and trying to satisfy the sword's appetite since it drains Hotsuma's life force was intense and very memorable for me.

Mundus from the original DMC. The aerial battle, followed by the one in the lava pool, and the surprise return close to the game's completion was memorable and fun.

Finally, Alama from Ninja Gaiden/ NG Black on Xbox (or NG Sigma on PS3). She was HARD, but man oh man you feel like a man when you beat her. Very fun, but challenging boss fight. It's as if she has no pattern, and that's what makes it fun since she's not as predictable as most bosses.

Puppet Ganon
Koloktos

Mother Brain - Super Metroid

It's hard to explain why it's so great without spoiling it for those who haven't played the game yet, it's something to be experienced.

Metroid Prime - (title drop)

Pretty intense fight overall, you have to constantly switch your beams to fight Metroid Prime while avoiding it's projectiles and rush attacks and finally Hypermode it to hell the Essence mode.

Ornstein & Smough - Dark Souls

The reason people fear Arnor Londo, and the reason you will die, a lot.

The Boss - Metal Gear Solid 3: Snake Eater

Not only do you have to prove that the student has finally become the master but you also have to do it before some MG-21s fly in and bomb the place, with the song, "Snake Eater" acting as your timer before they arrive.

Liquid Ocelot - Metal Gear Solid IV: Guns of the Patriots

The final fight to conclude the Metal Gear Solid (1-4) saga, complete with music, effects and animations from all four games, a pretty great way to wrap up the original pre-MGS V Solid series.

Bowser - Super Mario Bros. 3

It's short and sweet and to the point, it's definitely not too complex but it's a fun fight.

Mundas - Devil May Cry

They really went all out with this boss and it seriously feels like it's never going to end as when you get to the end of one crazy section another one begins. It's a great rush and it ends off the game quite nicely.

Xemnas KH2, both fights. "We Shall Go Together!"

Ganon OoT.

Mother Brain Super Metroid

Shadow Queen Paper Mario 2.

In that order.

These two have been my favourites for a long, long time.

Hercules in GoW3. What a knock-down, drag-out brawl between two equally Godly opponents. I like how he's not some huge guy you're hacking stuff off of instead it seems a lot more personal that way. Hades is also great for different reasons but damn I love destroying Hercules especially that finisher.

That is an honorable mention of mine. Also, take the title of the game out of spoiler text so people know what to look at or what not to look at. 

IKR? I had a lot of trouble on that when I was a kid, but I played the game again a few months back. Still had the same epic feel, just not the difficulty. 

Psycho Mantis
The Boss
Liquid Ocelot

Replayed MGS recently so these are the great boss fights I can think of.