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[Dustin Smith]

when i was three i thought yoshi's island bosses were epic.

+1 to the konjak and treasure love.

[Inanimate]

if there was a massive war between bosses from 2d games

THIS IS A GREAT IDEA

[Nitromatic]

I recommend 2D, as I am not big fan of this "three-dee".
And besides, two-dimensional, may it be platformer or top-down game, if done well they can be good gaming experience than 3D.

... Not sure what I am writing, dead tired, see?

[gunswordfist]

The final form is sidescrolling.

EDIT: Posting that video has reminded me why the Oracle games were amazing.

Brings back good memories. I still need to play Ages.

[gunswordfist]

see also, from the greatest action game of all time.

Nope, it'll always be 2nd to this game: http://www.youtube.com/watch?v=xsRZdyhoeB8

[moi]

Contra hard cops is amazing, it has enough bosses for 10 games. And there are alternate routes, actually I don't even remember fighting this boss.

anyway, something more ancient, one of the first mega bosses:
http://www.youtube.com/watch?v=s5PDf3R6zd4

[paste]

Legion from the Castlevania games, for sheer creepiness factor.
http://www.youtube.com/watch?v=UqxQpCqq1-o

This is one of my favorite bosses of all time.

[Strife]

With regards to your choice between 2D and 3D, I would definitely recommend 2D to start things off. Since you don't have to worry as much about that third dimension (except when pulling off visual stunts), it's easier to make a visually impressive and intimdating boss that keeps players on their toes.

As for examples, I think everyone here hit the nail on the head. xD If you're looking for a decent list of awesome boss fights, the Best Boss Ever page on TVTropes may be worth a read:

http://tvtropes.org/pmwiki/pmwiki.php/Awesome/VideoGameBosses

[Glyph]

The Nightmare or SA-X from Metroid Fusion. I can't think of more perfect examples of epic 2D fights.

[Strangeluv]

Nuff said!

[Jasper Byrne]

Revenge of Shinobi

[McMutton]

Revenge of Shinobi

I could never get to that boss. I always ended up lost in that damned maze.

[BadgerManufactureInc]

I completed it around age 14.
Hardest fight was the Master, if you lost one life you didnt get another chance, it was curtains.
His color changing wig was a dangerous weapon.

So much copyright infringement going on there, not just Godzilla but the Terminator, Spiderman and Batman.  They didnt seem to care in those days, considering indie games werent in existence and so AAA games just 'got away with it'.

Music was epic in that game too.

[archagon]

The Metal Slug series, especially 1-3, has some incredible boss fights. Most of them are pattern-based and very predictable, but oh-so-much-fun! My favorite, or at least the one I remember most, is the climbing thing from Metal Slug 2/X, stage 2 (Egypt).

Apogee's Stargunner is another game with great bosses, one for each stage. (About 30 total, IIRC.)

That's one of the things I miss from the 2D days of yore. Most 3D games just don't have the same sort of ginormous, what-the-fuck-style bosses, nor the immense feeling of catharsis you get from beating them. It was fun to go through each stage knowing that something terrible was lurking at the end, wondering what horrible tricks the designers would unleash upon you this time. Half-Life 1 is the last 3D PC game I remember that did it well. (Half-Life 2 utterly sucked in that regard.)

EDIT: Oh yeah! For more intelligent boss fights, see the 2D Zelda series, especially Link's Awakening and Minish Cap.

[Strangeluv]

Actually, probably every boss from Gunstar Heroes, especially against "Green" in Expert Mode