I like Ferries.gr because it shows how many seats are left in each booking class on a route (which is useful mostly if you book last minute), using an "at least 30 seats remaining" concept similar to the airlines J7/Y7 concept on EF. I then go and book direct on the specific company's website, which is recommended, because you get e-tickets and you can do ticket changes on the phone (at least for Seajets).