Company I used to work for before I went to law school insisted that all airline bookings had to be made through the in-house office of a travel agency, with airline tickets (this was before electronic ticketing) sent out by Federal Express. The tickets always arrived with stern warnings stapled to them that, if any changes were made, the employee will be responsible for all "additional charges."
It didn't take long to figure out that, almost every time, the tickets were on American Airlines, even though I was based in Houston and American Airlines was far from from the best option for most itineraries. In those days, of course, airline ticket coupons were pretty much like cash, so I would take the poorly-scheduled American Airlines tickets, which often included a change of plane in Dallas-Fort Worth or elsewhere, and exchange them for first-class tickets on Continental Airlines, usually a nonstop and, usually, with some money back to the company (although whether the company got it, or not, I don't know).
I don't know what the kickback was, but the travel agency seemed to have blinders when it came to choosing airlines, and they were terrible about even asking about, much less considering, the schedule of the traveling person. On a trip to Philadelphia and back, for an extremely modest savings, they had me connecting at Pittsburgh in both directions, rather than taking the easily-scheduled nonstop flights offered by Eastern Airlines. Honestly, it was kind of insulting.
Eventually, I learned to get very aggressive with travel desk, and while they didn't like it, I didn't much care what they liked.
