Vietnam forum

I agree with sarah about the train being the best option, even though it costs a bit more than the buses. You could do both sections by night train, and the sleeper cars are similar to European trains in size and comfort, while the long-haul buses are fitted with these coffin-like sleeper seats that even medium-sized people usually complain about.

I did the Hanoi to Hue by night train and quite enjoyed it, then later I did Danang to Nha Trang as an all-day journey, also in a sleeper car, and the scenery and ride were fantastic.

There's a lot of train information here on Travelfish, and even more info on Seat61.

http://www.seat61.com/Vietnam.htm

Posted from within Vietnam.

I think from Hanoi to Hue and from Hue to Nha Trang, you should go by train. It is cheap and safe and the beds are comfortable, too. On the train , you can enjoy many sights along your journey.
Mekong delta to Angkor , you can go by speed boat to Phnom Penh in about 5h. Arriving to Phnom Penh, you will continue go by boat to Angkor Wat

Or you could do what I am doing! Fly into Hanoi .I am doing a motorcycling trip starting 7th of Jan 2011. Hanoi to further up north and come back to Hanoi in a full circle and then ride all the way to HCMC and continue further to the southern tip. This way you dont miss an inch of land in Vietnam and 3 weeks are more than enough!