I worked for a US Multinational company which had a fairly good corporate travel department, if you got stuck somewhere in the middle of the night you could call the 24 hour number and they'd handle the rest rather then having to queue with people, and they'd inform all necessary parties in the company what was happening. Unfortunately that companies travel policy was always the cheapest, regardless of inconvenience.
The best guy I had was with my last company, he was an ex travel agent employed by the company simply to do all travel coordination. He fully understood the needs of those in the company and communicated properly on all bookings, and would keep you in the loop (i.e bookings that are held, and when we need to confirm and pay for them, once paid for refunding or transferred to next day etc), and also offer low cost airline flights when schedules were definate and it was the option between a 15 hour business class flight or a 4 hour direct Thomson flight (i.e Sharm El Sheikh to Manchester). The guy was working for the bigger picture, and not just to a budget.
In essence, when your travelling a lot, someone on your side can be invaluable especially when things go wrong.
On the flip side, if it's an outside company that adds extra to the bills and offers your a poor service then it obviously is going to be easier booking yourself.