Colin,
I am certain there are 100 ways to do it, here is my 2 cents; I just crossed this week (May 2016) on my bike from Thailand into Cambodia (and returned). Had it not been for my diplomatic passport, my thai drivers license, and my get out of jail free pass from the Minister of Foreign Affairs (MFA) I would not have been allowed to do so. The only reason I was allowed to pass customs in Poipet was due to diplomatic status (duty free import privileges). Cambodia does not allow foreign tagged vehicles to simply cross over - they must be temporarily imported and you need an agent to do so and it can be expensive (read bribes). Motorcycles were supposed to be the exception but that is not the case when you are in the customs office at the border. You need the proper paper work - but it can be done.

Another option - (one of) the quickest way I've seen is to simply buy and sell cheap scooters at each border crossing - sell the one you're on, cross over and buy another - they are cheap enough that in many ways it makes sense but that obviously does not apply to most readers here - but buying a cheap ride can easily cost less than a few weeks worth of taxi hacks and broken down bus scams in some of these places!

Keeping in mind what another poster mentioned, the border is very porous, it is very easy to cross countries in Asia when not on the highway, but you are at risk of being apprehended (i.e. Locked up Abroad, waiting on a Consular Officer visit from your embassy). Best to do the required paperwork and import the bike for your time in country.

Siem Reap was a great ride, I highly recommend Prassat Beng Mealea as a must see, it was so quiet it was spooky, and of course the 3 day temple pass ($40USD) did not apply up there but tickets were only $5USD ea.
we can take this off line if you'd like more/recent info
cheers
Mike