For WDW, they can do things like book your meals, and I believe they can book Fast Passes (if those come back). They will plan an itinerary for you to help you get the most out of your park time, and give you tips and hints throughout the planning process. They are always available to answer any questions you might come up with too. The agents have lots of experience with the products they sell, so they can always give advice and opinions form their personal experience.
While less planning is needed for a cruise, they will touch base with you from time to time to give you information pertaining to your cruise, whether it be on board venues/activities or ports of call. They will remind your booking window dates to be sure you don't miss out. I believe they would book activities for you if you would like, but I'm not sure on that. They can give advice and answer questions based on their personal experience and feedback from other clients...basically they help you get the most out of your trip.
And they always watch for discounts and automatically apply them to your reservation if any do come out that you are eligible for.
I do not believe they book air.