My favorite characters are Link, Zelda, and Tetra. Link is one of my favorite characters because in all of this misfortune that he goes through and is forced to save the world, he still gathers the courage to save the land. Also, even though he doesn't speak or anything, I always feel like his personality is still drawn out from his actions as a silent hero. He also is still "limp" enough to draw out a whole new, different personality from him whenever I write Zelda fan fiction so he's just one of those ideal characters who is easy to bend at will.
Zelda is also one of my favorite characters because of her personality. Even though Nintendo has been getting creative on her role as a princess and not being the traditional "damsel in distress," she still has this secret, bubbly side of her that especially comes out whenever it's a non-serious moment. She's also great comic relief (in Spirit Tracks), yet she still understands how grave a situation is and knows when not to be silly.
Tetra is on my top three because she's a tough girl who lived the life of a pirate, yet, she's still gentle and kind, as any princess would be. I especially love her part in Wind Waker and how there's a major plot twist including her and you're still thinking she's just a minor character who doesn't matter in the plot. But she does and I love how Nintendo made me really surprised about how involved she really is and how she is oblivious to it.