There are many sites out there that will compare airfares/hotel expenses/car rentals and give you the choices. There may be some limitations, however. For instance, the latest airline to do this is Frontier Airlines which penalizes passengers who don’t book directly through them. Not only that, they will get less frequent flier miles and not be able to book their seat until check-in. Another thing is if you don’t book through them, you will be charged for your carry-on baggage.
Southwest Airlines was the first to cut out booking on third-party sites. You won’t find American Airlines’ fares and selling tickets on Orbitz.com. Expedia is making American’s fares harder to find in protest.