My experience is eight years old now but just to give my feedback.
* Can Sambor Prei Kuk be done as a day trip from Phnom Penh?
I visited in a pretty easy part day trip from Siem Reap if that is any use. Early morning coach, easily picked up a return ride on a moped at the turn off near Kampong Thom. And I managed to find a space on a busy bus heading back in the early afternoon. But if you are stopping off there on the way it should be pretty simple side trip to make.
* Is there anything worthwhile in Phnom Penh?
Choeung Ek Genocide Memorial (aka the Killing Fields)
Cambodia's largest North Korean themed restaurant
(in case you miss the second largest in Siem Reap.) :)
* Reason I am asking is that I would like to do the river cruise from Siem Reap to Phnom Penh and would need to make some space in my calendar...
Just a heads up we had to abandon our plans to do a similar trip as water levels were low and that affected the time it would take.
* Is it hard to arrange transport to Preah vihear?
I had a Khemer speaking friend that was able to arrange it fairly easily for me. I would imagine the infrastructure has improved enough that a day trip will be offered by a few places around town (a quick google brings up a few expensive options, but I'm sure there may be other options available around town). This TripAdvisor forum has public transport info
, though it may not work as a day trip with the bus timings.
One thing I do remember is that the cost of the drive from the main road up to the temple was a pretty expensive km or so, but there aren't any other real options beyond a rather tiring, boring and potentially dangerous climb (there were mine clearing teams active all the way up when we visited, but then it was a semi active front line as well).
Siem Reap is really set up to cater for tourists, most things are available with a bit of asking around (and I would imagine that stretches well beyond finding a taxi and driver).
Give Angkor as much time as you can, it really is impressive. A decent chunk of a day to cover the main central parts Angkor Wat and Thom and the loop of temples around it is good. I would certainly recommend getting out to some of the outlying parts, Bantaey Srei shouldn't be missed and can easily be combined with a trip to Kbal Speen