Best - Ganondorf (Ocarina of Time), Twinrova, Bongo Bongo, Phantom Ganon.

Worst - The hand in the first Super Smas Bros

I'll preface by saying that I fucking love MGS3.. but the bosses in that game were schizophrenic at best. The End was great, fair enough. The Boss was great, but because of the story; it was cinematographically stunning, but in terms of gameplay it was pretty generic. The sorrow was a good experience, but not really a boss I guess?

Everyone else was a weird throw away character, which was a shame. MGS1/2 has great bosses (yes, even Fatman), but MGS3 felt like a mixed bag to me.

best boss: hades from kid icarus uprising
worst:polygon man from psasbr

If you consider those bosses unfair, you've never played old SNK fighting games, right?

Edit - OT - Best: Gene (Arena 51 challenge in God Hand), several Dynamite Headdy bosses.

Worst: - DMC 3 - Mission 19 - Arkham boss fight after Vergil joins.

God of War - Ares, after picking up the sword.

Suikoden V - Euram (+goons) boss fight in Sable.

Nope I barely played more than a round of any SNK fighter.

Well, I'll just say that this trope is named after them for a reason:

http://tvtropes.org/pmwiki/pmwiki.php/Main/SNKBoss

Best

The End MGS3. One heck of a fight the first time I played this, and it still resonates with me.

Psycho Mantis MGS. Total mind fuck back in the day.

Final Boss GOW:A The entire boss fight is one of the BEST fights I have ever experienced.

Almost every boss so I'm just going to post the box art. Shadow of the Colossus

Akuma Street Figher Ex Plus Alpha (PS1). You had to employ serious dexterity here. During the campaign you had to do extremely well on all fights leading up to the last boss. Instead of fighting Bison you would get this guy. A well executed boss fight, and FAR from easy.

Pretty much every boss fight was special here. I remember having to fight the moth boss over a lava pitt while fighting her minions and trying to feed my sword in order to prevent it from draining my life. Wow! Shinobi (PS2)

Worst

Polygon Man PSASBR (PS3) This turd tops the list. Super Bot SERIOUSLY threw away the chance to make an epic boss fight. Such a disappointment.

A bunch of the bosses here were crap including the statue of liberty, budda statue, bone dinosaur, the last boss, Dagra Dai, etc etc etc. Don't get me wrong I love the game, but some of the bosses were poorly executed. It's like they ran out of ideas and made the bosses stronger due to the lack of complexity. NGS2

Joker Batman AA  ... meh

Kefka from FFVI, Ganondorf from Twilight Princess and Heavily Armed Pokey with Giygas in Earthbound are some of my personal favorites.

Tomb Raider had one of the worst bosses ever. It was a great game, but what a crap boss fight.

I'll list them by game, not by the character itself.

Best:
- Ocarina of Time
- Majora's Mask
- Wind Waker
- Twilight Princess
- Skyward Sword (The last battle in this one was absolutely epic)
- Final Fantasy VI
- Chrono Trigger
- Pokémon Gold and Silver
- Borderlands 2
- Muramasa
- Metal Gear Solid 2
- Portal and Portal 2
- Super Mario Galaxy 1 & 2
- Tetris Attack
- Crysis |, Warhead and 2 (I haven't played 3)
- Silent Hill 2
- Star Fox 64

Worst:
I don't know.

both best and worst !