When you use a real booking system like Apollo or Sabre you can see more about the flights that you're booking (how many seat available in which fare code, etc.) as well as alternative routing strategies that can be *really* hard to find on leisure travel sites.

For example, when I book a trip for my client it is typically along the lines of this:

Amsterdam -> Doha -> Dubai -> Muscat -> Amman -> Amsterdam

With better info I could get better, more useful, connections and layovers. I would also be able to tell if flight A has no seats available in First Class while Flight B (which leave 45 minutes later) has 12 which means I'd likely book him on flight B so he'll have a better shot at an upgrade.

I'd also like to use it for my own personal travel as I like to do Mileage Runs and those can be next to impossible to plan well without a back-end system.

ETA - there's nothing wrong with Orbitz, etc. and they're great for 99.9% of things. But sometimes the extra info is great.