I started with Number9Dream, which was the Booker nominated that preceded Cloud Atlas. It's a great read, and I think probably his most accessible and entertaining. It's set in contemporary Japan, is very Murakami inspired, and each of the 9 chapters adopting a different theme. Great stuff.
Obviously Cloud Atlas and Jacob De Zoet are his more accomplished works, and you can't go wrong starting with either.
His original novel, Ghostwritten, has some very interesting bits, but definitely one of his weaker works, alongside the semi-autobiographical Black Swan Green. You can safely leave those until last!