They are much more difficult for a travel agency to book and ticket than regularly scheduled airlines. However the savings are significant enough that they cannot be ignored. Their best savings are to the Orient, with Europe, Africa, and South America just behind. They are not a viable option on domestic flights yet and they are also fairly ineffective to Australia. Booking is almost always done over the phone instead of in the computer.
Tickets are usually mailed to the agency, so last minute bookings are difficult.
Every travel agency uses different consolidators, so prices can fluctuate among agencies. Be sure to get several quotes and always make certain quotes include tax and any applicable fees. A fax or email copy of the itinerary which also shows the price is highly recommended. This is near the proposed strike dates for Delta and American, and if they both strike, seats on all planes will sell for quite a bit more than the cheapest fares. It would be very bad PR for the airlines to raise prices in this situation, but they can accomplish the same goal by simply removing the cheap seats from their inventory.