Oh dear, above poster, I think Stone Tower Temple is my favorite dungeon of my favorite Zelda game, but this is also slightly off-topic.
Favorite Ganon?
First off: I kind of think Ganon/Ganondorf is sort of an underwhelming villain. At least compared with the other villains of the franchise (which also aren't fantastic but w/e) he lacks the chaotic insanity of Zant or Majora or the nuance of Skullkid or ... Vaati?
In fact- all we see of Ganon in pretty much every game is the last fight- while his henchman do all the dirty work. He's distant, but in a bad way, and his triforce of power makes him into an ugly giant pig monster (or maybe he seeks the triforce because he is one).
Two exceptions exist: WW Ganon(dorf)- who's dialogue is much more interesting than the typical "grr.. I want power" and OoT Ganondorf where we see pre-ganon rule and post-ganon rule, not to mention various cutscenes which make him seem more fleshed out and an all-around better villain than other games.
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Pre-Post Edit: Oops, nevermind I just scrolled up and saw that you hadn't listed WW- rightly so- as it doesn't contain a Ganon but rather only Ganondorf. I guess the other posts got me confused. So disregard my psychological mumbo-jumbo.
I think I understand your post now- So to answer your question- OOT Ganon > all the rest. He's less an ugly pig and more... something else. Obscure minotaur? Dragon-ish? His ambiguous presence adds to the allure and his twin gold weapons are kinda cool. Twilight Princess had an interesting take on his beast form too but it was secondary to his human form.