Mine would be The Fear and The Fury.

The Fear is the best Boss battle in the game for me.
You can throw Rotten or poisonous food for him to eat.
When he is eating, I always shot him at least one time before he got away. But, sometime I he got away first while trying to shoot him. After he eat the Rotten or Poisonous, He will vomit which cause him to lose a chunk of stamina.

i loved fighting sniper wolf both times

I always thought the fights with Revolver Ocelot were great despite their brevity and simplicity. My favorite of the two Ocelot fights would be the one in MGS3 with that canyon between the men. I'm not sure if anybody here would consider it a boss fight, but that sequence when EVA drives the motorcycle and you have to fight your way out of Grozny Grad. Since Snake's eye was gone and he had the patch over it, I would take his shirt off, have him smoke the cigar, and shoot that big American assault rifle(the one he starts yelling with when you shoot it for awhile) in third-person view. He looks like an even bigger badass than he already is.

MGS1 - Ninja, Rex and Hind battles out of the three Ninja as Rex battle is too fiddly in PS1 version
MGS2 - Solidius battle is the only good battle in game, rest were boring in case of battle with Vamp, easy in case of battle with Olga, Stupid in battle with Fatman or in case of Fortune "battle", pointless
MGS3 - Best game of the three for battles due to technology that PS1 didn't have and that Gamecube didn't change in MGS1 and that Konami learned their lessons after shoddy boss battles in MGS2 as outlined above, however in this game I think that the battle with The Boss is the best battle in the MGS series but the battle with The Fear should get a mention as it is the funniest battle in MGS series by far due to feeding him food, making him sick and him squeeling "Fear" throughout the battle.
P.S. This is just an opinion and as far as you know a genuine one, please don't be offended by or attempt anything you have just read. This viewpoint was constructed by the inquiring and ever mercurial mind of Rzarector
Thank you

Metal Gear Solid 2: Battling against Solidus and...

Metal Gear Solid 3: Battle with The Fury (I like the darkness and all).

quote RZARECTOR

MGS1 - Ninja, Rex and Hind battles out of the three Ninja as Rex battle is too fiddly in PS1 version
MGS2 - Solidius battle is the only good battle in game, rest were boring in case of battle with Vamp, easy in case of battle with Olga, Stupid in battle with Fatman or in case of Fortune "battle", pointless
MGS3 - Best game of the three for battles due to technology that PS1 didn't have and that Gamecube didn't change in MGS1 and that Konami learned their lessons after shoddy boss battles in MGS2 as outlined above, however in this game I think that the battle with The Boss is the best battle in the MGS series but the battle with The Fear should get a mention as it is the funniest battle in MGS series by far due to feeding him food, making him sick and him squeeling "Fear" throughout the battle.
P.S. This is just an opinion and as far as you know a genuine one, please don't be offended by or attempt anything you have just read. This viewpoint was constructed by the inquiring and ever mercurial mind of Rzarector
Thank you

The Fear was also the easiest.

vamp was weird, with his popping up out of no where (the snipe part)

I liked the Fury, how he would scream if he couldn't find you. It really felt like he was a scary killer coming after you. They way he got mad if you shot him, it's really different from any other game.

The End was fun the first 2 times but after that it's long and pain.

Mantis was a cool fight, so was the solidus fight but it was too repetitive.

The End Is so much fun... or maybe Vamp And Solidus in MGS2 when there in the jet...

The End and The Fury are tied for first. I couldnt possibly choose second

I agreee, the fury battle was spectacular and ace to watch.

And The End was a classic battle of slow brooding violence, where you have to wait, and move and survey for that. one. perfect. shot. And the moment the end appears in the crosshairs for the first time was just a rush of 'There he is' and you realise you finally have him

Liquid Snake on top of metal gear in MGS1