I stayed at this place when there last year: http://www.peaceofangkor.com/

Cheap, safe and comfortable with an enthusiastic but not overbearing staff. Just out of town (about 5 minutes walk). The owner is a photographer who knows where to go for great photos and can organise tours as required. They will pick you up from the airport as part of your booking with no extra cost.

I flew from REP to SIN on Jet* Asia with a quick stop at Phnom Penh. Cheap enough and no problems.