Blizzeta was my favorite for Twilight Princess.
First off, all the bosses were way too easy. This detracted from the experience for me a lot; bosses are suppose to challenge you. Also, I had little to no trouble figuring out how to hurt the lot of them, so there wasn't even a decent puzzle for me.
Narrowing it down, my two favorites would be Stallord and Blizzeta, but Stallord was again way too easy, and way too short. Yes it made use of the creative Spinner (which I love), but it also fell short on maximizing it's potential, and the fight suffered greatly. There just wasn't any depth.
Overall I think Blizzeta was the best combination of unique idea, great atmosphere, and a little challenge. I thought in some ways Snowpeak Ruins was one of the game's better dungeons because it was actually a little hard for me, and while Blizzeta didn't really challenge me, she was harder than most if not all of the other bosses, IMO.