Assuming the purpose of your visit to Angkor is to do more than tick off another one of those "must see" places, planning your visit can be a bit daunting. There are more than 40 identified sites in the Angkor Archaeological Park alone, plus a dozen or more ancient sites within a few hours' drive from Siem Reap. Figuring out which sites you want to see, and in what order, can be quite difficult. On this page, I'll try and give you a few ideas about how to plan your trip.
Planning your day: Firstly, it's good to know how the typical day is organized, at least for private tours. Even in the so-called "cool" season, the middle of the day can be quite hot, especially when trudging up and down rough stone stairs - remember, this is where the "temple-mountain" evolved! For this reason, most guides will arrange for an early start - 8:00 am or earlier - for a morning session, and bring you back to town around lunch time for a break to eat, relax, and maybe even take a dip in the pool (many experienced travelers consider a pool to be an essential hotel facility to have in Siem Reap). Your tour will resume later in the afternoon, typically not before 2:00 pm. On at least one day, it's typical to observe the sunset at one of the temples.
Transport: Many people underestimate the size of the park. Remember, this was once a city of as many as a Million people. Some visitors think that they can "just catch a cab there and wander around." That is so very wrong, and not just because there aren't any taxi cabs that you can just flag down. To give you an idea of the scale of the place, keep in mind that the enclosure wall of Angkor Wat is 5.5 kilometers (3 ½ miles) long. So, you need transport, which can be either an air-conditioned car, or a motorcycle-cart. These are usually engaged on a daily basis. See the getting around page for daily rates. Don't worry about finding them; they'll find you.
Guides: As much as I enjoy and promote the idea of independent travel, I have to say that having a guide can greatly enhance your first-time experience of Angkor. A good guide will be able to arrange your schedule to get you to the places you want to go when they're not crowded, as well as suggest some other places based on your preferences. Guides will generally organize transport for you. The very best guides are Ponheary Ly and her brother Dara. You can find their contact information through a Google search. Note that all guides are supposed to be licensed. A licensed guide will wear a uniform of a beige shirt. Be wary of any guide that shows up without the uniform.
What to see, and when: Now we come to the crux of the issue; what to see, as well as the best times to see them. You have to decide for yourself what sounds most interesting, but of course there are some basic "must see" things. First and foremost, of course, is Angkor Wat temple itself. Since the temple is one of the few that faces west, rather than east, "conventional wisdom" is to visit it in the afternoon. However, while there is the long causeway and several out-buildings to the west, the central sanctuary itself is completely symmetrical. Approach the temple from the east in the morning, and you'll see more or less the same thing that you'll see in the afternoon. Exit by the west so you still see the libraries and other buildings.
The old royal city of Angkor Thom is the next "must see" location. Specifically, after a short stop at the south gate to cross the naga-lined bridge and walk through the four-headed gateway, the enigmatic Bayon temple is the center of attention. Here again, the typical advice is to see the Bayon in the morning light. However, like Angkor Wat, the Bayon is very symmetrical, so an afternoon visit will be just as photographic as a morning one. If you have the time, and the interest, I can highly recommend a late afternoon walk from the Bayon, through the Baphuon to the Phimeanakas and up to Preah Paililay before ending at the Terrace of the Leper King. If you're really into these temples - and even I have to admit this is a bit extreme - you can continue across the open field in front of the terraces and on to the Preah Pithu group, the Prasats Sour Prat and the Kleangs.
The last stop on a "minimal" tour would be one of the temples that are still in the partial embrace of the jungle. Ta Prohm is by far the most popular, which can be a drawback. It can be hard getting a feel for what the first Westerners saw when they first encountered the temple when there are several busloads of other people about. Good alternatives are the massive Preah Khan and the much smaller Ta Som.
The minimal tour will take just a day. With more time and the desire to explore, you can add a trip out to the charming Banteay Srei as well as visits to the temple-mountain of the East Mebon and the distinctive Neak Pean. The Roluos group would be another good option. The really ambitious will want to spend a whole day outside the park visiting Kbal Spean and Beng Melea.