FWIW - I'm just back from Siem Reap (end of September 2008), and my 2 cents on some of the things discussed above:

On Malaria: the locals aren't taking malaria meds as a preventive measure, so why would you? I travel in SE Asia for about 6 months out of each year, and have consulted with embassy and military doctors in a half dozen countries over there. Do what you like, but the consensus has been that unless you are camping or living in open air bungalows, you are wasting your money and subjecting your body to unnecessary drugs. Use DEET when you are in areas with lots of mossies (which also prevents Dengue and other assorted nasty things), but otherwise don't worry about it.

Rainy season: I was there at the height of the rainy season and we didn't see a drop in 2.5 days in Siem Reap. During my three weeks in PNH, there were some heavy rains, but they typically did not last for more than an hour. The rains will make travel more difficult if they hit at the wrong time, but most of the time it appears that the worst case is you would sit one out for a couple of hours and then resume touring. I'll trade that risk to avoid the huge crowds that are apparently there during the high season.

Guide: Don't skimp, get a guide, and read http://www.theangkorguide.com/ before you go to get the most out of it.

Hotel: I stayed at the Prince d'Angkor for around $55 / night (including breakfast). It was nothing special and the service was lacking compared to what I am used to in SE Asia, but it was clean, the AC worked, the pool was fairly nice, and I didn't get sick...

TJ