I flew in to Phonm Pehn from Bangkok for a few days then took the boat to Siem Reap and flew back to Bangkok out to Siem Reap.

I say take the boat. You can ride a bus anywhere, but I agree don't sit inside the boat. Small space and lots of people and the motor is very loud. Bring H2O and a small snack. Try to get a space sitting on the roof or the rear of the boat (outside) and enjoy the sites and sun. I had a tour guide waiting for me when we arrived in Siem Reap. He was holding a sign with my name on it and we got into an air conditioned vehicle and headed to Angkok Wat. Probably costs me $25 a day tops for escorted tours (including vehicle, dirver and lunches) The road to Angkok when I got off the boat was in very poor condition, just dirt and dust and the poor folks that took a rik-shaw (open bicycle taxi), had to breath that dust and dirt. I could see them with their shirts over their nose and mouths.

Enjoy!