Business or First Class would definitely be worth using an agent for, economy class fares usually don't have the profit margins to allow much room for discounting.
Be careful of using lesser known internet only agents often located in Eastern Europe, their fares often come out cheaper with the search engines but at the final stage of booking, additional fees and taxes get stuck on which sometimes make it cheaper to book directly with the airline. Also they have been known to go bust or disappear without passing your money onto the airline. Paying by credit card gives some protection but doesn't help when you are forced to rebook at short notice.