I am a travel agent -so I book them myself through my airline system. With the exception of Southwest and other "exceptional" carriers, Allegiant, etc. I have never seen a better rate online than what i can get in my system (and I always check). Of course most agencies will charge a booking fee.
The other benefit to using a travel agent is if things go wrong mid journey. Over Christmas, Continental cancelled my bros' flight and rebooked him 3 days later. I was able to rebook him on American leaving in a few hours and get the CO agent to endorse the ticket to AA. My bro didnt' have to pay a cent for what would have been a 1200 non-stop flight on AA.
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