For "planned" travel (dates and destination set) Hotels, Expedia and Orbitz in combo with hotel and airline proprietary sites i.e. the rates on the travel sites are often the same as the proprietary sites so research on one, book on the other. Priceline is good if you are very familiar with the destination, just pick high star ratings.
For unplanned travel i.e. Eva needs a break to get away, Jetsetter is often fun.
PRICELINE ...you can either choose the flight hotel or car you want exactly or you can BID YOUR OWN which means you gamble with the rate you wish to pay...you save up to 60% off the original rates..sometimes hotwire treats me a little better than PL but all in all they are both great sights on various days
The fact remains if you wish to complain with 3rd party agencies it is most difficult to change your reservations, so I would go direct & cut out the middle man. Miss Bliss AAA has awesome discounts on hotels, and travel. Call me when your back in SD. Let's do lunch lovely lady we miss you!