LifeinAsia - 6:28 pm on Mar 25, 2013 (gmt 0)
Most likely you'll have to use APIs to hook into the booking engines of the different affiliate programs. On the backend, call each respective API and combine the results before outputting the results to the customer.
You'll have to make sure that doing this is not in violation of each partner's ToS. Many (most?) have language in place to prohibit this type of comparison shopping because of the load it places on their sites.