A tough choice. There's been so many memorable boss fights. A couple standouts would be the duel with Kratos from Tales of Symphonia, Quadraxis from Metroid Prime 2, and Wesker from Resident Evil 5. I won't get into the context much of the duel between Lloyd and Kratos, but suffice to say, it is truly a crowning moment of awesome. The pre-fight conversation followed up by an incredibly fast-paced duel with an amazing song to back it up (The End of a Thought) made it more memorable than the final boss fight.
There were a ton of great fights in the Metroid Prime Trilogy, but Quadraxis had enough foreshadowing and buildup to really get you scared. In the Light world of Aether, you see these giant parts for a robot, and scanning them reveals that there were more than just one of them. And these pieces are huge. Then you get to the Dark World's boss chamber, and you see this giant quadruped robot that would make an AT-AT look conservative. The fight is long and arduous, but the weapon that you get from beating it is oh so sweet: the Annihilator Beam. Probably Metroid's coolest and overpowered weapons.
And then there's Wesker. The fight was kinda crappy because of RE5's idiotic controls, but the music, this crazy orchestral piece that sticks in your head, made it worth it. Plus being able to do a combo which has Chris brutally beating Wesker into next week is so gratifying to pull off, even if it's done with a freaking quicktime event. And I might as well put on this list the duel between Yuri and Flynn near the end of Tales of Vesperia. The fight's somewhat tough, but the music is once again an awesome and the dialogue between Yuri and Flynn is beyond hilarious. And if the controls weren't crap, the fight with Proxy near the end of the Force Unleashed was also awesome. Just when you think Proxy's used up all his holographic tricks, he breaks out Darth Maul. And then Duel of the Fates kicks in, and it leads to the best part of that level...right before the motherf**king Star Destroyer.
Boss fights are what we make of them. Some are epic, some aren't, and others are engraved in our minds forever.
