I'm kind of love-it-or-hate-it with boss battles, honestly. I'm more of a 'level' guy, myself. I prefer maneuvering through deadly obstacle courses. Still, a good boss is a bracing, exciting experience. The best boss is probably one that pushes you pretty hard, but only takes a couple of tries to beat, while being somewhat superficially impressive. What have been your favorite boss battles over the years?

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More recently, Zelda has had some phenomenal ones. Twilight Princess: Stallord, Argorok, and Morpheel. All epic, my favorite probably being Argorok and that fight's sense of height. And the last boss in Spirit Tracks was crazy .
An "older" one that sticks out is RE4's lake monster when you're on the boat. Good stuff.

The Colossi, which was the meat of SotC.

Though I do like the final battle in OoT. The fight with Ganon is amazing because of the music and presentation, it really sets you up for THE final battle.

I thought the boss fight at the end of Dead Space was pretty satisfying.

Pretty much the entirety of Metroid Prime. Super Metroid too, though they were all a bit too easy to be super satisfying.

Shadow of the Colossus, pretty much every boss was amazing, and I especially loved the flying ones. Though that's not quite fair, since the game IS just a bunch of boss battles, so they damn well better be good.

No More Heroes had a lot of great ones, including Shinobu, and um... the last two (don't want to spoil anything).

Zelda games have had some great ones.

And um... the fish at the end of the first stage in Earthworm Jim 2. Yeah.

My most memorable/favorite boss battles from recent memory:

Eox - The Legend of Zelda: Phantom Hourglass

Cragma - The Legend of Zelda: Spirit Tracks

Solar Satellite - Starfox Command

The Shinra Army - Crisis Core: Final Fantasy VII

Any pretty much any assassin from No More Heroes. (I'll post more as I think of them)

Kefka's final form in Final Fantasy VI was excellent. Bowser in Super Mario 64 was pretty epic as well.

Final Fantasy VI - every fight with Ultros; especially his lines with each fight. I like how during the final battle with him, he's like "No seriously, this is our last battle"

Resident Evil 4 - I liked a lot of fights in this game, but Chief Mendez definitely stands out to me. I love how he transforms so rapidly into such a disfigured shape, and the atmospheric music that plays during his fight. It's pretty freaky

Mega Man X - Sigma's first form is completely badass, especially with that music!!

Deadly Premonition - The epic boss fight against the Raincoat Killer is so cool. I love the badass music that plays during it

Contra III: The Alien Wars - Choosing a great boss in this game is tough, but I'll go with the alien dragon thing that attacks during the boss run at the end. The fight combined with the music is so intense

Oh and I remember loving the Starfox 64 dogfights against Starwolf and crew. Actually a lot of the other bosses in that game were pretty sweet as well.

Zero said:

Oh and I remember loving the Starfox 64 dogfights against Starwolf and crew.

Looks like we win today, Starfox.

Oh boy i remember fighting hitler in wolfenstein, the cyberdemon in doom, demogorgon and the dragons in baldur's gate 2, FF6 in general, and now the god of war series.

EarthBound: Giygas
Zelda series: Helmasaur King, Twinrova, OoT Ganondorf/Ganon, Goht, Molgera, TWW Ganondorf, Stallord, Argorok
Final Fantasy 3: Kefka
Resident Evil 4: Chief Mendez, Verdugo, "It"
Metroid series: Crocomire, Mother Brain (Super Metroid), Meta Ridley, Quadraxis

Can't believe you guys remember all these names.

I really liked Metroid Prime in... Metroid Prime. Modern Zelda bosses are really cool, but usually too easy. I did enjoy Zant in Twilight Princess. What a freak. And that horsehead boss from Zelda II left a lasting impression.

Now that I think about it, Punch-Out did "all boss battles" before SotC or Alien Soldier, or whatever. But maybe you could say that for fighting games, as well. Like Yie Ar Kung-Fu.

Anyway, Festivus reminded me of Hitler in Bionic Commando. You didn't even fight him, but that payoff... holy hell. Captain America and Superman wish they were that hardcore.

Those WWII comics were pretty funny. But it might be cool to do a realistic (!) take on what a World War would be like with partisan and non-partisan superheroes involved. I'm surprised no one's tried it yet.

A few in no particular order:

Earthbound/Mother 2 - Giygas
The Legend of Zelda: Ocarina of Time - Ganon
Final Fantasy VI - All fights against Ultros
Resident Evil 4 - Chief Mendez
Chrono Trigger - Lavos
Metroid Prime - Meta Ridley
Doom - Cyberdemon
Shenmue - Chai
The Legend of Zelda - Aquamentus