Final Fantasy X - "Otherworld"
This theme plays once at the start of the game and again much later during an important boss fight. There's something liberating about fighting a boss to a metal theme while being constricted to turn based combat.
Mega Man 2 - "Dr. Wily's Castle"
This track has achieved stardom through fan remixes and internet hype. Even if you don't know what game it's from you probably have heard the melody once or twice.
Sonic 2 - "Dr. Robotnik's Theme"
This theme reappears throughout the original Sonic titles.
Super Mario Galaxy - "Attack of the Airships"
This song plays typically when Mario is boarding a Bowser airship. This theme reappears throughout the Mario titles and effectively captures the power at Bowser's command. Bowser seems to have a different theme for every game he's in but the airship track best represents his own empire: The king of reptiles with thousands of minions and a fleet of flying airships at his command. Every title in the series seems to start the same way...Bowser already has captured Princess Peach.
Bravely Default - "That Person's Name Is.."
This might be the only boss theme on the list that I could describe as pretty as well as badass. An instant classic that gets your adrenaline pumping.
The Legend of Zelda: Ocarina of Time - "Koume & Kotake"
"Koume & Kotake" (better known as "Twinrova") have one of the best themes in the Zelda series. Combining just the right amount of creepy and playful, this song accurately describes their role as tricksters and the matrons of Ganondorf. The award for Most Likely to be Featured in a Clown Nightmare goes to the "Koume & Kotake" theme.
Final Fantasy VII: Advent Children - "One-Winged Angel"
Remixed for the CGI sequel to FFVII, One-Winged Angel is the theme song for an ascended Sephiroth. Both VI and VII themes allude to the villain's power comparable to a god.
Chrono Trigger - "Battle with Magus"
There's nothing like playing this for the first time and watching flames light up the pathway to Magus. You can hear the wind whistling as he tries to summon Lavos.
Sonic the Hedgehog (2006) - "Solaris 2 Theme"
It's a shame this great piece of music was wasted on such a poor game.
Donkey Kong Country - "Gangplank Galleon"
Starting off lighthearted as you enter the pirate king's domain, the theme soon gets a little more serious with those long '80s-cop-movie-esque tones. So, so satisfying to hear that "KRUNK!" as you nail King K. Rool with a monkey jump.
Castlevania: Dracula X Chronicles - "Bloody Tears"
This theme plays throughout the early Castlevania titles, but unfortunately has found no love in the series reboots. Maybe it's a little too upbeat for the darker theme of vampire hunting, but one of the series' best nonetheless.
Super Mario RPG: Legend of the Seven Stars - "Dodo's Coming!"
A quirky theme for a unique fight. Mario is poorly disguised as a statue and must remain incognito inside a baddie's castle. Instead of the typical "fight," Mario must dodge pecks and continue to look like the other statues while a big dumb bird waddles around looking for you.
Final Fantasy VI - "Dancing Mad (Full Song)"
Many debate that this theme and Kefka as a villain are the best in the series. "Dancing Mad" is a work of art. It consists of four different movements that some describe are Kefka's last speech: The first being his realization of ultimate magical power, the second being his twisted satisfaction in killing for fun and without purpose, the third acting as the villian's mockery of "meaningless" things like religion and art, and the fourth detailing the final stage of the fight and the eventual sadness that comes with Kefka's realization that it's all over.
Conker: Live and Reloaded - "The Great Mighty Poo"
With titles like Banjo Kazooie and Donkey Kong in their library, Rare has always been a childhood favorite of mine and really command fantastic soundtracks... But the boldness of Conker's Bad Fur Day takes the cake. I can fairly say this is the first and last time I've heard a pile of feces sing opera at me. Definitely a unique fight to go with a hilarious theme.
God of War III - "Zeus' Final Stand"
This is the culmination of the last three games. Kratos has extracted his revenge on all but the most powerful of the gods and now faces his father Zeus.
Super Mario 64 - "Bowser's Theme"
Something about this theme just makes me envision Bowser wearing black sunglasses and a spiked leather jacket.
"So long King Bowser!"
Pokemon Black and White / Black 2 and White 2: "Elite Four Theme"
This track perfectly sums up the culmination and peak of your time as a Pokemon trainer: The fast paced exhilaration that comes from facing the hardest challenge.
Star Fox Assault - "Star Wolf Theme"
The minor antagonists of the Star Fox series and direct competitors of Fox McCloud and his crew.
Shadow of the Colossus - "Revived Power"
A lot of work went into the music of boss fights in this game, and so much is said using only musical cues. Rightfully so, since SotC really only consists of bosses and travel time between them. This music celebrates that moment when you find the weak point on these beasts.
Banjo-Kazooie: "Final Battle"
Here's a great example of a final boss theme that instills a rushed, pressured feeling important to most final battles while maintaining the overall feel of the title you played. The final battle with Gruntilda still keeps the quirky sound of the overarching game with musical references to your past experiences.
Turtles In Time - "Boss Battle Theme"
Phoenix Wright: Ace Attorney - "Cornered!"
The "boss" fights mean so much in the Pheonix Wright series as they are the literal culmination of all the work you ever did. You line up your evidence just right and make that defendant sweat their way into jail.
Super Mario Galaxy 2 - "Final Bowser Battle"
I wish this fight was harder or went on longer so players could really hear the whole thing once or twice. You can hear the same sort of chorus most likely inspired by the Super Smash Bros. Brawl main theme.
Super Smash Bros. Brawl - "Main Theme"
In practice, every fight in Smash Bros is a boss fight and this is by far the best one. Nobuo Uematsu was contracted specifically to write it.
The Legend of Zelda: Ocarina of Time - "Final Battle Against Ganon"
OoT was a darker game for the console it was on and this song really drove that point home. Later Ganondorf/Ganon fights in the series have been much more lightly colored and less ominous sounding. While trading in a memorable melody for an atmospheric standoff, it worked wonders in instilling the feeling that you were really fighting an ancient and most powerful evil.
This truly is the definitive Ganon fight and one of the many reasons this game is a timeless classic.