I threw in the 13 cents just for fun. Seems the big guys figure a monopoly is better. See the report on this website. Well not quite, but ever since I used web sites to book travel, I have always used multiple sites to shop and then typically go to the airline to but the actual travel.
The trend is to combine elements of the trip (air, hotel, ground transport) or order to "package" a better price. While that might occur sometimes, I have found that to not be the case sometimes. It can be cheaper (and more convenient) to book each piece separately.
Back in 4 June 2012, I wrote about the hassles from using one of these sites. In my trip earlier this month, I combined air and hotel on the airline site, after exploring multiple airlines, connections, costs, convenience for the air, and several sites for the hotel, including the hotel itself.
One thing that I am really sensitive to is connection times in airports, especially if you need to clear customs.
So I think we got a good price, timed the way we wanted it and when and where we wanted to go.
With the airlines merging and developing partnerships, be sure to include them in the search for travel.