Southwest Airlines is the only major airline you cannot book on any of the all in one booking sites listed. I have included links for airlines that can be booked through these sites because there can be advantages by booking directly with the airlines. Links for international airlines can be found on the Trip Advisor website - see All in One Booking Website section.
All in One Booking Websites - Airlines, Rooms & Rental Cars
Hotels and Motels
Mant hotel groups and booking websites offer extra rewards or discounts. I will try and include as many hotel/motel booking websites as possible, excluding websites for specific hotels or motels.