Hudson is the obvious #1, he's just plain awesome. Mulder and Zito are pretty much the same player stats wise. Personally, I'll take Mulder who has proven he can win games without getting a lot of K's, unlike Zito.
What is so "obvious" about Hudson being the #1?
Zito Cy Young in 2002
Mulder may have won it last year if not for the hip.
Both have proven that they can dominate for extended periods. I think that Zito can bounce back. The three are separated by an eyelash for me.