This is a topic I could prattle on about at great length. I could, but I won't. I'll limit myself to three.
Del Lago - Resident Evil 4
Honestly, any one of this game's boss fights could be here because they are all, without exception, incredible. Del Lago was the giant monster on the lake and anyone who says modern Resident Evil isn't scary has obviously never fought this boss. It was like playing the movie Jaws but only the monster was five times bigger and it was twelve times more tense (I had a professional multiplier run the numbers for me, these are legit figures). Armed only with a mysteriously endless supply of harpoons and your own urine soaked trousers you had to fight this humungous beast while it dragged your boat around and tried to eat you, succeeding on many an ocassion I'll be willing to bet. This boss fight absolutely nailed atmosphere and tension and to be a stand-out boss fight in a game with nothing but stand-out boss fights is quite an achievement.
Blind - A Link To The Past
At least I think it's called Blind. I'm talking about the boss from the 4th Dark World dungeon in ALttP. You're lead to believe the maiden of the dungeon is locked in a cell and not in crystal like the others. In hindsight, I really should have seen this coming but when I was 5 years old I couldn't even put my own socks on so you'll forgive my naivety. The boss room is clearly marked on your map but nothing ever happens in there so I spent some time wandering around utterly baffled. You need to use a bomb on a bit of weak floor in the room directly above, causing natural light to shine into the boss room which forces the maiden you're escorting to reveal her true form, Crazy-Eyes-Red-Ball-On-A-Sheet-Man (or Blind as I may be mistakenly calling it). The actual fight itself is very challenging and well done but it was always the build up to it that I loved. It was completely unexpected and Nintendo have never done anything else like it as far as I can recall. It's things like that which create lasting memories.
Stained-Glass Demon - Medievil
Medievil and Medievil 2 had some amazing boss fights but the Stained-Glass Demon always sticks out in my mind. It's not a particularly difficult boss by any sretch but it shows the game's style and creativity really well. I mean, how often do you encounter a demon made from the stained glass of a church window? Someone who's seen a bunch of mad anime is probably gonna link me to a website which specialises in the discussion of stained-glass demons now aren't they? Well, regardless of if there are more, it was unique to me. I love Medievil and I love it for things like Stained-Glass Demons. I love it for things like Pumpkin Kings and dragons that think they're Sean Connery and for elephants that swim underwater and for Canny Tim and for Dirk Steadfast and for Jack of the Green and for having a chicken drumstick as the most deadly weapon available. There was a real soul to Medievil and it shines brightest with moments like the Stained-Glass Demon of the Hilltop Mausoleum.