I expected to see this crop up after the Desert Island thread. This one is awfully hard, but here is my list in (today's) order1. Blood On The Tracks. I consider this to be the masterpiece he told us he was going to paint.
2. Blonde On Blonde. I think that most of Blonde on Blonde is wonderful.
3. Freewheeling. His first almost entirely self-penned album, a real look at the brilliance to come.
4. Bringing It All Back Home. So this may not be a popular choice on the Mudcat, but this album was the start of the electric Dylan. What a start.
5. I'm going to suck out here and go with the Bootleg series. I know it's three CD's, and I don't like everything on it, but the moments of brilliance that are captured over the thirty years are some of my favourite creations.
Honourable mention to Highway 61, Oh Mercy, Time Out Of Mind and Love and Theft.