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There is almost never a reason to buy tickets through a travel website. Use them to check airfares and compare, yes. But then go directly to the airline site to buy, you'll save the travel site fees and sometimes can even find even better fares. (This is especially true for hotels lately, where a lot of the chains are offering exclusives only through their sites.)
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I noticed this as well.
sidestep.com finds some great prices, its one site to least check first to see what airlines are flying in/out of certain cities with the best prices. Then check out those individual airline sites.