Things to keep in Mind: Broadly speaking, there are two types of temples around Siem Reap, monastic complexes and temple mountains. Try to include both types in your itinerary. Also, some temples have been restored and some have been left basically as they were first discovered. Again, try to visit examples of both. Finally, the temples were built over a 400-year period, and the building style and materials evolved over this period, so try and visit both early and late period examples. Angkor Wat and Bayon (in Angkor Thom) are both unique in their own right and are must-see's, no matter what your planned route. Try and include any sights that are dependant on the weather as early on in a multi-day visit as possible. i.e. don't leave a sunset climb of Phnom Bakheng until the last day just to have it rained out. Try and visit the temple mountains early in the day, when it’s cooler. Steep climbs are required, and there is little shade at the top. Visiting the monastic complexes can be done through midday as there is plenty of shade.
Before you go: Pick up a guidebook that details the bas-relief carved at Angkor Wat and Bayon; it will be invaluable. If you decide to use a guide, speak to them first. The level of English fluency and knowledge varied dramatically among the ones I saw at the temples. Also, when booking a driver, make sure he understands your itinerary, as they may expect additional money to visit some of the farther out temples or for a very long day that goes from before sunrise to after sunset.
Considering all the above factors, my ideal route (and close to the one I followed) would be: Start the day at Angkor Wat to watch the sunrise from the north lotus pond. Move immediately on to Angkor Thom (you’ll comeback to Angkor Wat in the afternoon, when the bas-reliefs are better lit.) for a quick walk along the Terraces and chance to admire the South Gate. After that, head out to Banteay Srey, stopping at Ta Keo, Pre Rup, and East Mebon on your way out. Then come back towards Angkor Thom and do a long walk From Sras Srang through Banteay Kdei and Ta Prohm. This should take a couple of hours and carry you through the midday heat. Have your driver meet you at the west end of Ta Prohm so that you don’t have to walk back. From here, move to the bas-reliefs at Bayon and Angkor Wat, but still take the time to enjoy the temples in their own right. Then end the day with a climb up Phnom Bakheng to watch the sun light up Angkor Wat as it sets.