There is much to be seen in this part of the world that you need to plan to return several times & prioritize.
Based on my preferences & experience, I would first go to Angkor (must see), 3d at least. And would give priority to Hanoi over Ha Long Bay (same moutain range but much more fab scenery in China, near Guilin, on the Li River).

It is monsoon season, so I suggest Bali as a good alternative.. They are just coming off high season

Anyplace else is SE asia that won't be monsoon-ing?

Weather is weather, it's unpredictable.
Have a look at some of the Trip Advisor discussion forums.
Have a look at, and mess about with, weather forums like Wunderground.
Monsoon weather may slow you down a bit, but a bit of seasonal weather might also encourage you to linger a bit, and enjoy places that you might have wizzed through. These places are often the most memorable.
Stay flexible with your itinerary, and enjoy!

Vietnam with it's long narrow shape apparently offers a variety of weather at any given time..depending on your tour choices. I haven't yet been there but it certainly looks an interesting option for September.. October.

Sometimes it can be perfectly ok to visit some places in the rainy season. prices will be lower, it will be less crowded, the scenery will be greener. and, as an example, Angkor Wat is much better visited outside of the dry season for all of the above reasons.

Weather patterns are changing and monsoons are increasingly erratic do not always arrive when expected and your planned trip is on the cusp of the seasons in a number of places making decision-making that much more difficult if weather is of major importance to you

There are many whether sites around, some good, so not so good. This one has some good generic info http://www.bbc.co.uk/weather/features/18877641

and this is a relatively new site which has a lot of info [although some countries have not yet been added to the site] http://www.timeyourtrip.com/countries

@crellston<<<Sometimes it can be perfectly ok to visit some places in the rainy season. prices will be lower, it will be less crowded, the scenery will be greener. and, as an example, Angkor Wat is much better visited outside of the dry season for all of the above reasons.>>>

No doubt Angkor will be quieter during the rainy season.

BUT, as soon as it rains these historical monuments all become an extremely slippery invitation to get a broken arm, broken leg, cracked skull, or worse.

Approach with care!

I'm with Crellston on weather, rainy season brings it's own delights, don't get hung up on the monsoon.

If you've never seen a tropical downpour turn streets into streams, you're in for a treat. Then, you have a good excuse for spending some time in a coffee shop people watching.......

We spent 3 weeks in the Northern part of Vietnam in Oct one year, I recall 5 or so rainy days out of 21.
It doesn't always rain all day either, but as LL says, the ground gets slippery or muddy and I take extra care when walking around.

Bali is a great intro to SE Asia, scenic with friendly locals.

Possibly true LancasterLad but I tend to credit people with the common sense to know when not to do something. The rains generally tend to come in short sharp bursts and the monuments dry out quickly due to the heat.

<<<Possibly true LancasterLad but I tend to credit people with the common sense to know when not to do something.>>>

Even Korean tour groups? How many tourists do you hear or read about who've done something absolutely stupid that they wouldn't do at home? Many leave their common sense back on the aeroplane.

Often accidents that happen due to slippery surfaces aren't caused by the person who's got hurt, but by some other idiot not exercising due common sense who slips and crashes into them. Places such as the Angkor historical park when it's wet are prime venues.

Nice short video here...

http://www.youtube.com/watch?v=vIhhK_kLRwI

If we sought to eliminate all risk we wouldn't leave home.

Yep. But in unfamiliar surroundings it's wise to get into the habit of continuous risk assessment. Especially so in places like Angkor, where the excitement of being there, and following the flow, can easily lead to mishap, particularly if it's wet or looks like raining.

There's no need to eliminate all risk. Simply assessing the possible risks and acting accordingly usually does the trick.

Don't be put off by the monsoon/wet. It doesn't rain all day or even every day. The rain flogs down for an hour or so about 3-4pm, clears out the humidity for a nice evening, and then flogs down again about 8pm. We live part of the year in Darwin, part in Singapore, and part in southern NSW, and I don't mind the wet, it's an interesting season.

2 weeks are a nice amount of time! I was in Siem Reap for a week, it was a slow (no rush) vacation but I loved it! but if you want an efficient trip, i think you can travel between Cambodia-Laos-Vietnam-Thailand in 2 weeks

<<<I think you can travel between Cambodia-Laos-Vietnam-Thailand in 2 weeks.>>>

pink-fatamorge. I'd love to see you post an itinerary that'll cover all four countries in 2 weeks. Absolute bonkers imho, but please prove me wrong!