I've only beaten 2 dungeons, and my favorite is the Goron Mines boss. I was stunned by the amazing graphics for that boss. It was fun too. The Forest temple boss wasen't so great. I also really liked the Goron Mines itself.
Dragon cuz he was so damn hard for me and Zant because it kept you hooked I wish it lasted longer though and Ganon he was fun because your a tiny little wolf and you can take a huge beast hand-to-hand or Paw-to-Paw
Zant By Far! If You Can Read My Tiny Avatar, It Circles Zant And Sez MONG! Hes Is Mental, He DOes The Matrix And Twists His Body Round Like 720 Degrees! What A Retard!