I have just booked us into the Raffles Hotel Le Royal Phnom Penh for the end of November. When trying websites such as Expedia, and others, I was getting a big daily surcharge of £40+ on top of the £96 per day quoted. Expedia say this is due to local taxes!
Booking direct with the US based main booking office we were told taxes were around $15.50 per day per room - that is, less than £8. Also, if you book 21 days ahead the hotel has special rates which, even if you add on a full breakfast, is still less than the so called 'best rates' these websites quoted - though this is not cancellable.
For some reason we did not have this problem when booking in Siem Reap.