Overture to the End (https://www.youtube.com/watch?v=tGlp2-s-yLg) – From Mario & Luigi: Partners In Time. Plays when battling Princess Shroob. This is my favorite boss theme from the Mario series. Koopa’s Theme (https://www.youtube.com/watch?v=MBOsi1sMHoc) comes to a very close 2nd for me cause of it’s badassness.
Gangplank Galleon (https://www.youtube.com/watch?v=lS7_tcwsj4E) – Best Donkey Kong boss theme. Thought it was cool that it got remade in SSBB too, but I still like the original better.
Mechanical Battle (https://www.youtube.com/watch?v=4WmtlZVYx48) – From Separation Anxiety. With Guns Blazing (https://www.youtube.com/watch?v=FGYnuAdF3TU&list=PL3048995BAD07442E) also kicks ass.
Vs. Meta Ridley (https://www.youtube.com/watch?v=nLLjibR_c4Q) – From Metroid Prime. Best version of Ridley’s them in my opinion. Omega Ridley’s Theme (https://www.youtube.com/watch?v=VcpVyER_UTA) is also pretty cool.
Majora’s Mask (https://www.youtube.com/watch?v=4AzNTt-boS4) – Probably one of the most, if not the most menacing boss theme I’ve ever heard.
The Grave Digger (https://www.youtube.com/watch?v=OMJK-yffn5o) – From Resident Evil 3: Nemesis. Probably the most menacing boss theme in the Resident Evil series in my opinion. I always get a chill down my spine whenever I listen to this.
Phantom Ganon (https://www.youtube.com/watch?v=N8g7lxYwIHU) – From The Legend of Zelda: The Wind Waker.
All I got for now…
Face to Face (http://www.youtube.com/watch?v=5SHOvWhti98&list=PL54484A7672FDB135) and Tor (http://www.youtube.com/watch?v=86IxmklUgEM&list=PL54484A7672FDB135) from the game Iji (http://www.remar.se/daniel/iji.php) (The Last Link goes to the page where you can DL the game and the HQ version of the soundtrack.)
I also enjoy listening to the boss (http://www.youtube.com/watch?v=TUGBW3Qc4K4) themes from (http://www.youtube.com/watch?v=_hQzTkv_hck) Super Metroid. Though they can get a bit repetitive.
Metroid Fusion also has a few I like:
-Boss Room (http://www.youtube.com/watch?v=pVffc8czwes) (Not Sure if it counts, since you’re not fighting a boss yet! LOL!)
-Serris X (http://www.youtube.com/watch?v=oDjqxwbo7Mg)
-Core X (http://www.youtube.com/watch?v=9SZf0ACRt_Q&list=PLCE419A1BA49FC03B)
-Nettori (http://www.youtube.com/watch?v=2ZJCVuJqOas&list=PLCE419A1BA49FC03B)
And one of the best Boss themes out there, IMHO is Yell Dead Cell (http://www.youtube.com/watch?v=GkWBzXLJXrY) from Metal Gear Solid 2: Sons of Liberty, closely followed by Father and Son (http://www.youtube.com/watch?v=O-XbpCJxM9s) and the Battle Theme (http://www.youtube.com/watch?v=4xHnCtZ_OGg) from the same game.
Perfect Dark had an entire soundtrack in it’s favor, and the Boss themes seemed to be a more "urgent" version of the level themes.
Then, going into the 8-bit/16-bit arena, I like the boss music from the following:
-Super Mario 2 & 3
-Ninja Gaiden 1 – 3
-Werewolf: The Last Warrior
-MegaMan 4 (So sue me! LOL!)
-Batman
-Sonic 3
-Forgotten Worlds (http://www.youtube.com/watch?v=PwhLzUijOPc&list=UUx5YkPNQWMLFbv059WGp1sA) (Link is for the Arcade ver, but I played on Genesis)
-X-men & Spiderman: Arcade’s Revenge
-Maximum Carnage (especially the Super Villains (http://www.youtube.com/watch?v=U5raE8lvquA) theme) (I deliberately used this version so you can see WHY I like this track!)
…and at this point, it starts to become a list of games I’ve played over my 31 years of life.
Super Mario Bros 1-3
Super Mario World
Turtles In Time
Killer Instinct
Street Fighter 2
Maximum Carnage
– choir of curse (Boss BGM -type1-) (http://www.youtube.com/watch?v=2-lqNeL1Rf4) [Chaos Legion]
– Hiruko (http://www.youtube.com/watch?v=M73JHnx13LE) [SHINOBI ~ PlayStation 2]
– Phoenix (http://www.youtube.com/watch?v=E28ie3Xj4ek) [EHRGEIZ: God Bless the Ring ~ Quest Mode]
– The Final Hour (http://www.youtube.com/watch?v=3coOvRq_vkk) [Onimusha 2: Samurai’s Destiny]
– Ultra Violet (Nelo Angelo Battle) (http://www.youtube.com/watch?v=atGcliA-HNw) [Devil May Cry]
– BUST THE BEAST (Goatling/Phantom Battle) (http://www.youtube.com/watch?v=ADpec7QkoIw) [Devil May Cry 2]
– Beast Legacy (http://www.youtube.com/watch?v=n45Ks4ctmJ0) (Maybe not a Boss-theme in the strictest sense of the word, but it’s the track you hear on the last stage of Story Mode)
– [B]Theme of GOUKI remix (http://www.youtube.com/watch?v=BGUx6t87j-U) [Capcom vs. SNK 2: Mark of the Millennium]
Anything from the Tohou series
Megaman X5 – Final battle with Sigma
Final Fantasy 8/7 – Final battles
One-Winged Angel
FFVIII
Premonition
Maybe I’m a Lion
The Legendary Beast
The Extreme
FFIX
Dark Messenger
Necron’s Theme (Final Battle)
Chrono Trigger
World Revolution
One-Winged Angel
…
Chrono Trigger
World Revolution
I would have added these if I’d thought about it, but it also reminded me of the FF6 Battle Music, which I’ll add to my list…
Megaman Battle Network 4 – Battle With Myself ~ Boss Theme (http://www.youtube.com/watch?v=R0GLuDuiSzU)
Castlevania: Symphony of the Night (Saturn) – Bloody Tears (https://youtu.be/tgkxSkF7QOU)
Secret of Mana – Oracle (https://youtu.be/TCUdhcRQMC4)
Contra: Shattered Soldier – A True Last Boss (https://youtu.be/obayUKdauS8)
Contra: Shattered Soldier – Survival of the Fittest (https://youtu.be/N_gRBR-K-nY)
Sonic Adventure – Open Your Heart (https://youtu.be/qH_MCPcjxP0)
Sonic Adventure – Fight for My Own Way (https://youtu.be/JVqNzDRSLyY)
Super Metroid – Mother Brain (https://youtu.be/nBYlXtRjj34)
Super Metroid – Samus’ Theme (https://youtu.be/Hx4Gsp5rcwM)
Super Contra (arcade) – Hotter Than Hell (https://youtu.be/LumT49MNcAI)
Super Mario Galaxy 2 – Decisive Battle (https://youtu.be/8vxLzHSfnxk)
Super Mario Galaxy – Bowser (https://youtu.be/IObwdOCAfdU)
Megaman X8 – Last Boss (second form) (https://youtu.be/urdyRHAzIFM)
Raiden DX – Go to Blazes! (https://youtu.be/RfiOD_ctjcQ)
Final Fantasy 6 – Dancing Mad (https://youtu.be/JbXVNKtmWnc)
Super Mario RPG – Fight Against Kajidoh (https://youtu.be/HBRrzwvpaNQ)
Mega Man 2: The Power Battles – Mecha Dragon (https://youtu.be/d4IQL5OMRa8)
Super Castlevania IV – Dracula Battle (https://youtu.be/AbRWDpruNu4)
Super Castlevania IV – Simon’s Theme (https://youtu.be/pQVuAGSKofs)
Castlevania: Dracula X Chronicles – Dance of Illusions (https://youtu.be/_SWPBRpPfyc)
Castlevania: Bloodlines – The Vampire’s Stomach (https://youtu.be/llWhTJG6H-4)
Castlevania 64 – First Struggle (https://youtu.be/X2M5J1xzB7o)
Final Fantasy Origins – Battle Scene (https://youtu.be/bgDBa_eLlW0)
The Legend of Zelda: A Link to the Past – Ganon (https://youtu.be/LfISliRCnO0)
The Legend of Zelda: A Link Between Worlds – Yuga Battle (https://youtu.be/Oxl-n80bq_Y)
The Legend of Zelda: Link’s Awakening – Last Boss (https://youtu.be/554DNmPdbCc)
That’s probably enough until I think of more.