My favorite Link is Ocarina of Time Link. I enjoy the dynamic of switching between Young Link and Adult Link, and I think there are some pretty emotional moments like leaving Kokiri Forest for the first time and reuniting with Zelda when she reveals herself in the Temple of Time that really add to the memorability of this Link's character even if his design has been improved in subsequent installments.
Favorite Zelda is a tough one, but I'll have to go with Skyward Sword Zelda. I think she looks cute, and she does quite a bit more in the story than some of the other Zeldas in the franchise. Honorable mention to Spirit Tracks Zelda for being a useful companion as the Phantom.
Best Ganondorf is definitely from Twilight Princess. I'd also say he's the best Ganon. The fight is just too good, even if it is easy. I love going through all of the phases. First, the energy volleyball, then fighting Ganon as Wolf Link, next the horseback riding battle, and finally the sword fight. I also love just how imposing Ganondorf is in the game. The cutscenes where he kills the one sage and when he emerges from the castle after defeating his Ganon form give me chills.
