The T-Rex in pretty much every game I've encountered it like Tomb Raider, Dino Crisis, and especially Peter Jackson's King Kong. The T-Rex rules!
The lake monster in Resident Evil 4
Zero in Mega Man X 2 & 5 - He's a total badass and has awesome music. If you take too long to beat him in X5 he starts using a screen covering, one hit kill attack and essentially becomes unbeatable from that point on. He's THAT overpowered.
The Beastector members in Mischief Makers and every boss fight involving them.
The Necromancer, the Medusa, the ice level boss, and the giant Catfish in Castle Crashers
The colonel in Rockman X 4
Area 4 boss in Rez
Gambit in X-Men Wolverine Origins
Spontaneous Bootay in South Park The Fractured But Whole and again in the DLC.
The final boss fight in Super Daryl Deluxe
Dreadnought battles in Starlink Battle for Atlas, which are far cooler than anything I've ever seen in an actual Star Fox game.
Clayface in Batman Arkham City - The best boss fight in the Arkham series, unless you count the awesome Scarecrow sequences in Arkham Asylum.
Sniper Wolf was the coolest boss in Metal Gear Solid
King K Rool in Donkey Kong Country and Donkey Kong Country 2
Pretty much every boss in Three Dirty Dwarves
Fighting Shadow in Sonic Adventure 2
Every boss fight in Shinobi (PS2)
Apocalypse and Onslaught from X-Men vs Street Fighter and Marvel vs. Capcom