Hmm... hard to categorize definitively, as different fights often play out differently in context, and some of my favorite games i may not have especially loved for their boss fights, and similarly some fights, while quite difficult, may not be my "favorite"
Tossing out a handful of five that come to mind, we have:
Jhen Mohran (Monster Hunter Tri): Monster Hunter was all boss fights, all the time (unless you were ore-mining), and yet Jhen Mohran truly felt like a boss among them, even compared to the other "legendary" monsters of the game, Alatreon, Deviljho, and Ceadeus. A huge and thrilling fight that incorporated strategy more deeply than any of the others in a game that was all about huge and thrilling fights
Metroid Prime (Metroid Prime): Here was a boss with fairly simple tactics at its disposal, yet who remained compellingly difficult and was just plain satisfying to smack down, especially as you yourself received your ultimate weapon (Phazon Beam).
Egg Emperor (Sonic Heroes): He was the final boss of the main story lines, preceding the boss of the "final" story, and you saw something rather interesting here in terms of beat-down satisfaction and the ability to fully test the limits of the team combat that Sonic Heroes set forth. Although Heroes was fairly far down in my list of top 50 games, this fight stands out.
Goht (Majora's Mask): Having never owned Majora's mask and only loaning it from a friend, Goht stands out amongst all of the franchise that i have played so far (though Koloktos and Demise from SS, as well as Zant from Twilight Princess also are worth mentioning). Goht just created tension in the most delightful way.
Bowser (Super Mario 3D Land): it may merely be because this fight is fresh in my head, but this fight really put a lot of good stuff together compared to other Bowser fights from other games. Bowser fights have always been good about creating a sense of urgency, but 3D Land's final fight stands out because it is more varied and manages to really keep you on the edge of your seat. NSMBWii also did a good job of this, but less so than 3D Land did, now that i really think about it.
Monster Hunter: pissing me off since 2010.
