Southeast Asia forum

So you've got four months -- August & September see good weather (in the least) on Ko Samui and Ko Pha Ngan and Ko Tao in Thailand, the east coast of Peninsular Malaysia and Bali/Lombok in Indonesia. October is middling and by November both of southern Thailand, Laos and Cambodia will be shining while parts of Vietnam will be getting wet. So it needn't be a wet trip throughout

So, broad strokes you could do something like:

* Fly into Bali: 2 weeks: Bali/Java (beaches, culture, history)

* Fly out of Jakarta to Kuala Lumpur (I know you didn't specify Malaysia, but it fits in well) and head over to the east coast islands - Perhentians perhaps, say one week all up taking you to late August. If Malaysia doesn't appeal at all, look at flying something like Jakarta -> KL ->Surat Thani and going to Thailand's east coast islands.

* Back to KL, fly to Bangkok. coupla days there, then overland north via Ayutthaya and Sukhothai to Chiang Mai then head to perhaps Chiang Dao or Pai for a bit of trekking then overland to the Lao border Huay Xai - allow 2-3 weeks for this taking you to mid to late October.

* Cross into Laos, slow boat to Luang Prabang then Vang Vieng then Vientiane then Tha Khaek (for Kong Lo loop) then 4,000 islands then to Cambodian border. Allow 3 weeks for this. So middle of Nov.

* overland straight to Phnom Penh then south to Sihanoukville then to the islands (just pick one as there are quite a few - you can read about them here) then back to Phnom Penh, Siem Reap for Angkor Wat then overland back to Bangkok for flight home. Allow two weeks - end of Nov.

Wait, I forgot Vietnam!

To fit Vn in I'd suggest ditching Malaysia but that only gives you a loose week - you could conceivably overland from Phnom Penh for a taste of the south around Ho Chi Minh City ... time runs out quick doesn't it!

Further reading
Stops between Bangkok and ChiangMai
ChiangDao getaway
Trekking in Thailand
Elephant trekking in Laos

And here is a sample regional itinerary and there are a bunch of other ones linked to on that page - may be useful.

For budget flights see Air Asia, Tiger Airways, Nok Air and Jetstar -- all can be quite affordable if booked well in advance.

Cheers - more questions, ask away.