If you want a clean and decently equipped room in Phnom Penh, particularly near the river, Paddy Rice works. It's not a luxurious spa-retreat but it's not bottom-of-the barrel, either.
I often do dirt bike riding in Cambodia and between trips I want to have a decent room in Phnom Penh. Paddy Rice will be my go-to place from now on. I got the top floor "deluxe" or whatever, the one with windows on two sides. Nice room and the price is fair enough, especially since it includes breakfast.
The music downstairs is outstanding, and stops at midnight so you can still get a good night's sleep.
Location is great if you want to visit local nightlife, as well.