I've read that it's best to bring your own passport sized photos for the Cambodian visa and the 3-day Angkor Wat pass. How many photos do we need for each?

Just one photo each. We had more made because I thought I had read somewhere that you need two for the visa, but nope, just one for the Cambodian visa, one for the Angkor Wat pass, (and one for our Laos visa also). If you don't get them made ahead of time, it's very easy to do in Thailand. We had ours made at the first camera shop we popped into in Chiang Mai - about $5 as I remember for about 8 photos each. Took about 10 minutes or less.

At angkor Wat they will make the photo right there. I offered one of my own but they preferred to take it themselves because the process from taking the photo to the ID card was completly automated (using my photo would hhave added steps).

They did happily use my photo upon arrival at Siem Reap, however.

at the angkor entrance we did not even get out of the car as we had our photos and the guide just took them inside and was out if two minutes with our passes which have the pic embedded in them...

It's just one photo for the Angkor pass, but people have reported sometimes one, sometimes two photos for the visa. In my experience, it never hurts to have a couple extra passport photos with you.

So, we should be cool if we bring three each then. We don't need them for Malaysia or Thailand, right?

Right, no need for the photos for Malaysia or Thailand.