Wind Waker is my favorite Zelda. I've played and beaten it at least three times now, but alas, I lost the game disc for it, so I'm hoping to get a HD remake of it someday. Or if they put it on the VC for the Wii U, I will be happy. It would be fun if Nintendo decided to continue with that cartoonish Zelda on the 3ds.
For games that look potentially better using cel-shading I'd say Persona 4 Arena takes the cake.
Zero Escape: Virtue's Last Reward = best game ever made.