Bosses in Twilight Princess

Mini Boss Appendix

 * Ook (and Baba Serpents) - Forest Temple
 * King Bulblin (Round I) - Hyrule Field
 * Dangoro - Goron Mines
 * Shadow Bird Rider - Lake Hylia (drained)
 * Twilit Bloat - Lake Hylia (filled)
 * King Bulblin (Round II) - Great Bridge of Hylia
 * Deku Toad (and Toados) - Lakebed Temple
 * Skull Kid (and Puppets) (Round I) - Sacred Grove
 * King Bulblin (Round III) - Bulbin Camp
 * Death Sword - Arbiter's Grounds
 * Darkhammer - Snowpeak Ruins
 * Skull Kid (and Puppets) (Round II) - Sacred Grove
 * Darknut - Temple of Time
 * Aeralfos - City in the Sky
 * Phantom Zant - Palace of Twilight
 * King Bulblin (Round IV) - Hyrule Castle

Boss Appendix

 * Twilit Parasite: Diababa
 * Twilit Igniter: Fyrus
 * Twilit Aquatic: Morpheel
 * Twilit Fossil: Stallord
 * Twilit Ice Mass: Blizzeta
 * Twilit Arachnid: Armogohma
 * Twilit Dragon: Argorok
 * Usurper King Zant
 * Ganon's Puppet Zelda
 * Dark Beast Ganon
 * Dark Lord Ganondorf, Part I
 * Dark Lord Ganondorf, Part II

Boss Names
The dungeon bosses of Twilight Princess each have names that are twists on other names, with the exception of the bosses of the Palace of Twilight and Hyrule Castle:

Diababa is a twist on Deku Baba. Also, the prefix "dia" can mean "more than one", like in "dialogue". The Diababa has more than one head.

Fyrus is a twist on Darbus, which is the name of the Goron patriarch who was transformed into Fyrus, and the word fire.

Morpheel is a twist on Morpha, the boss of the Water Temple in Ocarina of Time.

Stallord uses the prefix "Stal", meaning any animated skeleton, and the suffix "Lord", to make Stallord, meaning that Stallord is "Lord of the Stals". Stallord is the largest stal encountered in the Zelda series, greatly surpassing the size of the Stalfos warriors in The Wind Waker.

Blizzeta is a play on Yeta, the female Yeti who becomes Blizzeta, and the word blizzard.

Armogohma is a play on Armor, for the the hard exoskeleton on this boss, and "Gohma", the insect-like boss that appears in several other Zelda games.

Argorok is a play on "Kargarok", the bird-like enemy that is common throughout the game.