This was my first trip to Crete, and it was last-minute, so I booked a hotel online. Pension Eva had reasonable prices and was located in the Old Town of Chania, which was my main concern, since I'd be walking everywhere.
The hotel manager e-mailed me to find out when I'd be arriving and offered to let me check-in early and check-out late free of charge to accomodate my ferry times. He even fixed the free internet when I e-mailed him to report that it wasn't working when I arrived; he was always prompt with replies to my e-mails.
One of the negatives was that there is no front desk to the hotel. . You let yourself in and out of the main building and your room during your stay. So you don't get the personal touch or someone to ask for advice in person, but for those who want complete independence, it's perfect. Also, the room could have been slightly cleaner and better aired, but I understand that I was visiting during the off-season and only booked my room the day before my arrival.
Lastly, it was a good value b/c the room not only had two twin beds but a private bath, a spacious shower (a rarity in Europe), a kitchen table, closet, and small kitchenette with mini fridge and hot plate(though I would have appreciated a microwave). Great if you plan to save some money by buying food at the market or store and doing some light cooking for yourself.