I've been to Cambodia. I didn't go backpacking there but here's my $.02
Underrated-
Right now is the perfect time to go because it's so damn affordable. It's still off of the beaten path but tourism is growing exponentially. I could have arrived there with $500 in my pocket, lived like a king for a week, and came home with change.
I suspect one of two things is going to happen
1) Tourism will keep growing naturally and the prices of everything will grow with it
2) Thailand will finally have the coup d'etat that's been bubbling for a while, the country will become too hostile and tourists who would have ordinarily have gone to Thailand will look at Cambodia instead, then back to 1).
Mosquitos-
Some are nocturnal and others are diurnal. The different species carry different diseases. My supervisor caught Dengue Fever there and was a hurting unit for a short period of time. Malaria is there but only in certain regions. Contact your local health department for more information on this topic and to determine if you need to take any prophylactic medication. Definitely wear bug juice and dress appropriately.
Water-
You probably already know this but don't trust bottled water purchased on the street. I had one with a sealed lid and life was no bueno for about a week afterwards.
Food –
Tons of great food in Phnom Penh and Siem Reap and I can't really pick one restaurant over another.
Had a chance to eat a cockroach, a giant cockroach (tough to get it down in two bites) a small frog, and a mystery bug. I looked and asked everywhere but couldn't find a fried tarantula. My coworker found one at the night market in Phnom Penh so give that a shot if interested.
Phnom Penh-
Visit Camp S21 and the Killing Fields. I love museums and thought the National Museum in Phnom Penh was great but the one in Siem Reap to be even better. Russian market…. sigh…. it is what it is. Despite the aggressive salespeople and abundance of black market goods, I still found some nice items there.
Siem Reap –
Allow three days to visit Ankor Wat, Ankor Thom, and many others. If you are at all like me, you'll be templed out by the end of the third day but I don't regret investing the time. The backpacker district is friendly on the wallet. Had a few nice meals there and can't go wrong with $.50 beers.
Getting around-
In each town, I found a tuktuk driver who spoke fluent English and who seemed trustworthy early on. I hired them for the duration of the time I was in town and it made my life much easier. For example, when I was solo in Siem Reap, we negotiated $40 for three days. He was in tears when I tipped him an extra $20 on the last day. I hired him during the days and was on my own at night. Never had to pay more than $2 to get anywhere in town.
The bus system works well. The buses are clean, comfortable, and very affordable. On my bus trip from Phnom Penh to Siem Reap, the bus was half empty (or half full) and I had both seats to myself. On the ride back, I was seated next to Hagzilla and dearly wished that I had purchased both seats.
You can take the bus to Vietnam no problem.
Hotels-
No your eyes did not deceive you. You can stay at a nice hotel for $15-$25.
Good to know if you don't already-
Before visiting Ankor Wat, Ankor Thom, et al, it helps to have a basic understanding of Buddhism and Hinduism. I highly recommend visiting the National Museum in Siem Reap before visiting the temples; it really does a great job of explaining why certain statues are in certain poses and other nuances I would have missed otherwise.
I've never been backpacking in SE Asia so can't speak to that.
