My first thought for favorite quote was Linebeck's wish in Phantom Hourglass. After all the talk of treasure, he really just wants his boat back. It shows that he's learned some humility, and suggests that he'll go on to become the adventurer he always pretended to be. Thing is, that's less a favorite quote than a favorite moment, especially since I can't even remember the actual wording.
So I'm going to go with one of Link's optional responses from Skyward Sword, "Am I late?" and Impa's response, "No, you're just in time."
Link's line ties into his making an impressive entrance in that scene, and it functions well enough just on the level of a one-liner. But I also like how despite being someone who doesn't talk much and is pretty passive (face it, in most recent Zeldas, Link pretty much gets told where to go and what to do) he's semi-subtly standing up for himself to the person who's been dissing him all along, and Impa's reply shows her finally starting to accept him as the hero.
It's sort of a running theme in the game, come to think of it, as Groose has a similar experience coming to appreciate Link (and growing into a better person in the process) but if there's a single line or exchange that perfectly encapsulates Groose's character development, I can't recall it. Besides, that development is pretty one-sided. I don't think Link ever cared what Groose thought of him, whereas Impa... well, maybe I'm projecting, but when I read her lines about Link not being good enough, man, it stung. I recall Link seeming offended, too, but it's been a wile.
Honorable mention: "An ally of justice!" Because Wind Waker Link is just great.