A friend and I are about to do the opposite journey (Siem Reap - Ho Chi Minh) tomorrow! We are in Siem Reap just now! We asked about the roads between Siem Reap and Phnom Penh as we didn't fancy a repeat of the journey from Poipet to Siem Reap (which is horrendous!) and have been told the roads are now pretty good and it should be fairly comfortable. The owner of our guest house told us this and he has been very good for information so far! He even emailed us to warn about the scams that go on getting from Bangkok to Siem Reap. He also said the journey should take around 5 hours (Siem Reap - PP)
After a few days in Phnom Penh we plan on getting a boat to Chau Doc on the Vietnam side for a bit then onto Ho Chi Minh. This appears to be a reasonably comfortable and cheap way to go.
If you want we can let you know what the journey is actually like! I assume you will be arriving in Ho Chi Minh around the same time as us!