Couple years ago I flew a cheapie regional airline called Jet Star from Phnom Penh to Singapore and it was very budget (charging $2 extra just for blankets a pillow!) but new and well run. I think they fly over most of the area. Bangkok Air is also good.
If I had had time, I would have taken the boat ride from Siem Reap (Angkor Wat) to Phnom Penh instead of flying. There's a whole distinct culture around the Tonle Sap, and the only way to experience it is by boat. My Rough Guide from a few years ago says the boat is $25. (BTW - they mostly use US$ in Cambodia) Phnom Penh is not really worth staying any time, just a typical third-world capital, but it is the transportation hub, so you'll probably have to go through there to see the rest of the country besides Angkor.
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