I spent 3 weeks in Cambodia, and would strongly recommend not going with a tour company, as your agenda will be dictated by the tour company and you will pay for the priveldege.
Fly to Bangkok, loads of airlines go to Bangkok, so flights are cheap and lots of availability.
You can then get a flight from Bangkok to Siem Reap, which is where Angkor Wat and other temples are. There is a range of accomodation from cheap to very expensive. I would never get the bus here, as it takes all day, and once the bus leaves Thailand, and gets to Cambodia, it slows down and goes along a potholed road. I'd recommend flying everytime.
In Siem Reap you can sort out a guide and passes to the temples. You can negotiate with guides or hire a bike. In Siem Reap as well as seeing the temples, also go to Red Piano bar and Foreign Correspondents Club.
You can then get either a bus, train or boat to Phenom Penh. You can stop at Battenburg on they through.
In Phenom Penh you can go to Royal Palace and Silver Temple, S-21 and the killing fields. Few other places to go to in Phenom Penh, including Foreign Correspondents Club.
Can get a bus to Sinakouville, which is on the coast. This in a nice laid back piece of beach, which is a lot more relaxed than Thailand.
We did the above in just over a week, which was a bit rushed. You could have a very relaxing time doing the above in 2 weeks. Three weeks would probably be excessive. If you want to go somewhere for a week, I'd recommend Lao.