Only two regular ferry runs still operate in Cambodia -- Phnom Penh to Siem Reap and Siem Reap to Battambang. Boats no longer run north up the Mekong to Kompong Cham and we've heard the Ko Kong to Sihanoukville boat now only goes as far as Ko Sdech, making it close to useless for travellers (other than those heading to Ko Sdech).
The Phnom Penh to Siem Reap boat is worth doing once and once only. It is expensive (when compared to the bus), the middle of the trip is boring (you're in the middle of a lake with no scenery) and, if you sit on the roof, chances are you'll get sunburnt. Do it once then catch the bus back.
The Siem Reap to Battambang trip is much more of a lucky dip -- the quality of the boats varies from one day to the next, overloading is the norm, boats run aground regularly and occasionally sink. That said the Battambang portion of the trip is spectacular -- very, very beautiful. So if you're not too fussed about taking dodgy boat trips, give it a go. In windy, stormy weather though we'd go with the bus, as the shallow lake gets a big chop on it very quickly, making for a very uncomfortable trip.