AirAsia is the big budget carrier for getting around. If you book tickets in advance, they are often the same price as taking a (often terrible) bus. The Phuket-Chaing Mai flight in Thailand comes to mind - it's a 16-20 hour bus ride that might cost $30, or a flight anywhere from $40-$70.
Here's a list of the budget airlines:
http://wikitravel.org/en/Discount_airlines_in_Asia
The only problem with this approach is you have to book everything in advance, and if you miss a flight along the way, there can be some pain as u have to still get there to catch a flight out.
Check out my website for some cautions on taking "scam" buses from Bangkok to the south islands and Cambodia.
Peace,
Ryan