Tough call. Right now, Warbreaker is the best written–though The Gathering Storm is better, I think. I think that Way of Kings will be awesome too. But you didn’t ask for the best, you asked for my favorite. In that case, I’d probably have to say Elantris, as it was my first.
That answer was as of 2009. The specifics of the answer may be different, but the intent is still the same. I love each of my books for different reasons, but I’ll always have a warm place in my heart for Elantris
Another time I answered:
I’d pick MISTBORN 3 if I had to. But TGS and KINGS are both better than it is
Yet another time, this was my opinion:
The Gathering Storm is, by far, the best–and most difficult–thing I’ve written. It’s what I’m most proud of. For what is published, though, WARBREAKR has the best writing of anything I’ve done.