Aye, most 3d Sonic final bosses have two stages and thus two themes. First you have the epic final battle theme, then the refrain of the main theme for stage 2.
The entire Sonic 2006 soundtrack was great, too bad the game itself was very buggy and unpolished, it could've and should've been a great game but was obviously pushed out the door before it was ready.
AC4's final battle theme was cool, but I must say I prefer AC Zero and 5's respective final boss themes.
Some other really neat boss themes off the top of my head.
One of the boss themes from the first Witcher game.
From Freedom Planet
From Sonic 2 (Game Gear), think it may have been the first boss theme I ever heard (also, that first boss in Sonic 2 GG is rage-inducingly unfair, lol)
Here's another Robotnik boss theme, this one from my favorite 2d Sonic game
Baldur's Gate 2 expansion final boss
Skies of Arcadia had some really enjoyable boss themes that would change verse based on how well the player was doing.
But IMO, one of the most iconic boss themes is Bowser's theme from Mario 64.
(of course I recommend checking out this awesome cover of Bowser's theme)
I really like Asgores theme and Battle against a True Hero from Undertale, as well as various soundtracks from Mario. Though there was this one song from Kirby i really liked years ago, couldn't really remember the name of it though.