Also off the top of my head, but in no particular order:
Thunderbird, Zelda II: I don't even know why to be honest.
Trinexx, A Link to the Past: It's three-headed fun.
Barinade, Ocarina of Time: Run around, throwing the Boomerang, killing stuff left and right, electricity chasing you--it doesn't get any better than that.
Ganondorf -> Ganon, Ocarina of Time: Pitifully easy, yet thoroughly enjoyable.
Goht, Majora's Mask: Goron Mask FTW.
Majora's Mask -> Majora's Incarnation -> Majora's Wrath: Pwnage fun with Fierce Deity's Mask.
Twinrova, Oracle of Seasons/Ages: Possibly even more fun than the OoT version, at least if you have that ring that gives you traction on ice.
Onox, Oracle of Seasons: Such variety, and his dragon form was epic.
Gohma, The Wind Waker: I loved crashing the ceiling down on him.
Helmaroc King, The Wind Waker: A pivotal battle at a pivotal point in the plot. And I loved smashing his mask.
Vaati (all three forms), The Minish Cap: Not as hard as everyone made it out to be, but it was a good go and a great ending to an already great game.
Stallord, Twilight Princess: Spinner FTW.
Armogohma, Twilight Princess: Can you tell I really like smashing things?
Zelda, Twilight Princess: Yeah, I know it was the usual tennis formula. But hey, you're actually fighting against Zelda! And this tennis routine feels far more genuine and enjoyable on the Wii.
Clawgrip, Super Mario Bros. 2: Catch flying rocks and chuck them right back. It was a hoot.
Wart, Super Mario Bros. 2: Force feeding veggies. A unique concept, if nothing else.
The Koopalings, Super Mario Bros. 3: I loved them all. And miss them too.
Raphael the Raven, Yoshi's Island: 360, 'nuff said.
Baby Bowser, Yoshi's Island: Seeing him creep closer and closer, getting huger and huger, just about made me soil myself when I first fought him back in middle school.
Cut Man, Mega Man 1: C'mon, he's Cut Man!
Mecha Dragon, Mega Man 2: An epic intro he had.
Wily's hologram, Mega Man 2: I was actually fooled for a bit and wondered how he could possibly turn into an alien. Oh, and sucks for you if you run out of Bubble Lead. =/
Gamma, Mega Man 3: The last final boss in the classic MM series before they resorted to the generic disappearing saucer act. This thing was huge, and the music kicked ass.
Dr. Cossack, Mega Man 4: Only because he was being set up by Wily and fought for his daughter's life.
King, Mega Man & Bass: A boss fight consisting of five phases, stretching throughout the stage. You've got to give him props for that.
Storm Eagle, Mega Man X: C'mon, he's friggin' Storm Eagle!
Sigma Final, Mega Man X: No matter how much mastery I have over this game, no matter how effortlessly I can beat the rest of it, this final battle never fails to kick my ass every single time. I don't think any other game can claim that on me!
Morph Moth, Mega Man X2: He actually morphs out of a cocoon during this battle. And it's fun to burn his ass up.
Serges, Mega Man X2: Against his later version, I know a strategy that keeps me completely safe but reduces him to rubble.
Iris, Mega Man X4: A nice fight, and one of the more provocative plot moments in the series.
X or Zero, Mega Man X5: Best musical piece in the entire series, and playing as one of these two against your partner is MMX's very own version of Anakin vs. Obi-Wan. Awesome!
Sigma Final W., Mega Man X5: A giant head. But a fun battle, epic music, and the works.
Rainy Turtloid, Mega Man X6: So huge, but goes down easily enough with the right strategy.
Dynamo, Mega Man X6: It's fun to find the right way to exercise some serious ownage on him and get special items.
Sigma (both forms), Mega Man X7: These have got to be the most fun Sigma battles in the whole series.
Lumine (all forms), Mega Man X8: A true surprise villain, grand plot twist, epic battle, good dialogue, healthy challenge that doesn't overdo it--this is a good one!
Mother Brain, Super Metroid: This might possibly be my favorite boss battle of all time.
I also enjoyed most of the bosses in the original Donkey Kong Country.