Favorites? Hm... sadly I've never greatly cared for Link as a character... mainly because he's generally not much of one. A little generic, IMO.
But of course, that's generally how he's designed to be, a link between the game and player and all that. Although I'll admit that in WW and TP he had more of a character.
Anyway, back on track...
I'd say some of my favorites are... Orca, Tetra, the potion shop guy (Chu Jelly nut
), Quill, Medli, Salvatore and Ganondorf.
Orca was awesome. He was a tough guy but he seemed to me to have a big heart, and I thought he was very likable. Quill was awesome, defending Link and helping him out. Actually, the Rito were awesome in general, so noble and willing to help those in need. Medli was also very cool and I liked her character a lot. Then of course there's Tetra and Ganondorf. Tetra was the best incarnation of Zelda thus far, I think. She wasn't exactly a damsel in distress like usual, and was actually a fairly strong character. She also had a lot of attitude offset with great kindness, and was an overall cool character. Ganondorf was coolest in Wind Waker, I've always thought. He had a much cooler, more dramatic aspect to him, and there was the never before shown "human" aspect to his character. I really liked that. In other games, especially Twilight Princess, Ganon becomes little more than a cruel, inhuman monster. I liked the change of pace and it added a lot more solidity to his character, IMO.
And finally, a couple of the silly guys. The potion shop guy who was always raving about Chu Chus and Chu Jelly was awesome. All the sounds he made and his dialogue was great. :xd: And then there was Salvatore. He was the minigame guy on Windfall and Spectacle Islands, where he used paintings to represent characters, and would make odd sound effects with his French-sounding accent to go along with the games. I especially loved his "SPLISH" and "KA-BOOM" sounds. :xd:
As for picking enemies, my absolute favorite is the Chu Chus. These little buggers were awesomer than any other incarnation of the Chu Chus, and I love them better than any other enemy in the entire series. They're weird, cute, and a little creepy. And the sounds they make are the best! :xd: I'm also a big fan of the ReDeads in this game. Probably my favorite variation of them, because of their creepy, disturbing and inhuman appearance, and somewhat tribal design.
I didn't really care for any of the bosses too much, except for perhaps the Helmaroc King. He had a cool appearance (except for when you broke his mask and he looked like a chicken -.- ) and his role in the plot was very cool. Probably the most story-involved, non-final boss in the series.