The world of the internet has opened up an array of booking and search engine sights for international flights and hotels, but sometimes going to the inside sources can offer even better deals (still online).
Agoda is the hotels.com of Asia. They do offer hotels on an international scale, but we particularly used them while setting up our trip in Thailand. Be aware that they sometimes do charge you first night as a reservation deposit, but there are options for free canceling up until a week or two before. Just remember to read the details.
Sawadee is a Thailand only site offering an additional extensive list of discounted hotel rooms. The site also offers informationon transportation options, things to do and see within each of the provinces, and any other tourist information you could crave.
Air Asia is the Asian equivalent of Ryan Air in Europe or Southwest in the USA. They offer cheap hopper flights across Asia. The prices can be cheaper than expedia.com or any other American equivalent, especially if you will be traveling with minimul luggage.