Ooo. I have so many. I like nearly all boss music, but let me give some highlights:
Jak 2: Baron Praxis Battle 1/Metal Kor(they use the same track for both...

) I also like the one that plays when you fight Krew. Good tracks overall.
Jak 3: Dark Maker Terraformer(Final Boss)
Kingdom Hearts: ...Nearly all of them. My favorite boss themes areprobably "Guardando Nel Buio" which plays during the Final Boss, and Forze Del Mal, which plays when you fight Ansem-possessed Riku. I also like the Deep End, which plays when fighting Dragon Maleficent. One Winged Angel is fun too.
Kingdom Hearts 2: Same as the first. My most favorite is "The 13th Struggle" which plays whenever you fight Axel or Luxord. I also like "The 13th Dilemma" which plays when you fight most Organisation members... and "The 13th Reflection" which is only available in Final Mix 2 and plays when you fight digital copies of Organisation members. Overall, I like all the boss tracks here, from the start to the finish.
Legend of Zelda: Ocarine of Time: Freaking love the theme that plays when you fight Ganondorf. Fits the epic battle so well.
Legend of Zelda: The Wind Waker: I love the final boss tune.
Legend of Zelda: Twilight Princess: The five tunes that play when pwning Zant. I also like the final of the FOUR themes Ganondorf uses when you fight him.
Sonic the Hedgehog Genesis: I like the Final Boss Theme in the first one.
Sonic the Hedgehog 2: The Boss Theme is win.
Sonic the Hedgehog 3: Boss theme is, surprise, win.
Sonic Adventure: I LOVE Open Your Heart. I also like the first theme that plays whenever you fight Chaos. Also like the Boss Theme of Zero and E-101 Mach II.
Sonic Adventure 2: Hoho, my favorite game. Live and Learn is epic win. "Suitable Opponent" (plays during Tails/Eggman and Knuckles/Rouge battles) is also good. I also enjoy "Masters of the Desert" (plays vs. the Egg Golem and King Boom Boo), "Shut Up Faker!" (plays during the Sonic/Shadow battle in Green Forest), "For True Story... Sonic vs. Shadow", (the tune that plays in the second Sonic/Shadow battle), "G.U.N Mobile" (obvious what this is for) and also, "Supporting Me" which plays when you fight the Biolizard. Overall, I love this soundtrack. <3
Sonic Heroes: I love all the Team Themes(which are boss themes, as they play when you fight a team!), sans the one for Team Rose... *Shudders* I like the Robot Storm/Robot Carnival themes. I absolutely love What I'm Made Of, and Metal Madness. I also mildly like the vs. Eggman tunes.
Shadow the Hedgehog: Do want I Am All of Me. Moderate liking for the GUN Mobile remixes and Black Doom tune. I like all the boss themes here, but the liking is mild. Despite being a hardcore Shadow fan, I really dislike this game.
Sonic the Hedgehog 2006: While Sonic was in his death throes during this, the music stays pretty good for me. I love the Egg Cerberus/Egg Genesis tunes. Mephiles also has a somewhat enjoyable battle theme. Iblis was good too. 2nd place of all the boss themes, though, is Solaris Phase 2. Gotta love how SEGA usually delivers epic main/boss themes.
Sonic and the Black Knight: My favorite here is With Me, both the All Ends and Crush 40 versions. I love how it's a dark and emotional remix of
theme. Besides With Me, I greatly enjoy "Fight the Knight" which plays when you go to pwn King Arthur. Through the Fire is semi-okay.
Sonic Unleashed: Gotta love Perfect Dark Gaia, as SEGA once more pulls off a "remix/use the main theme as the boss theme" gimmick. I love the soundtrack here, especially the bosses. My 2nd favorite is Egg Dragoon, which I feel fits Sonic and Eggman's "final battle" quite well due to it's epic, uncertain and dire feel. I also like the Eggman Boss and Dark Gaia's Spawn Boss theme. The former especially because of how well they synced it to when the Egg Cauldron appears as Eggman speaks... the moment you see that ship, hear Eggman talk, and hear that theme start, you go "Oh... Fudge. I'm boned. T.T"
Sorry for the epic wall of text! /Fanboysim