Defiitely Hanoi, Nhs Trang and Hoi An. I wouldn't spend too much time in Hue - the citadel is interesting but it's not as attractive as the other places. I highly recommend travelling through Vietnam by train - it's really easy to do and the line goes right down the coast.
i agree with Mike. He is an expert here.
Shop around before you book. But keep in hand which boat you want to go,. There are a lot of books in Halong Bay. for 3 days 2 nights, you want 2 nights on boat or 1 night on boat,1 night at hotel. So that we can give you some suggestions, then you will know which boat will meet your demand.
Spend 1 day in Hue, I think it is enough, then take bus to Hoi An and Da Nang. Vietnamese people like Da Nang because you can visit Ba Na Hills, it is so beautiful as I know./