Consolidators or business travel specialists have all sorts of bulk fare deals that you won't find on the internet. They will generally charge a fixed booking fee, because, as johnny Colombia said, commissions are crap these days.

If you find a good agent, stick with them, they're an endangered species. Sometimes they mightn't be the cheapest, but in the long term they'll save you time and money and maybe get you out of a jam. When I'm stuck in a thousand long queue at a snowbound hub, my agent will sort out alternatives and hotels etc. Try calling Kayak in that situation.