I second the check out the shops thing...have a contest to see who can find the ugliest T-Shirt or souvenir (my girls once spent 4 or 5 hours in the Pittsburgh airport doing that when we had a delayed flight!!), eating is always a great time killer for my clan and since airlines never feed you anymore they will probably be happy to eat. Be sure to gate check your stroller so you are not lugging baby about for 3 hours. Also you can probably find some empty gate areas where he could get down and run a little.
Last week in the St Louis airport I saw the sweetest family with mom, dad and 5 kids that had laid a quilt down on the floor in the corner of an empty gate area and were having a picnic!! It was really cute. Mom had a soft cooler with the food and dad and one of the older kids had gotten drinks and brought them back. The little ones had room to wiggle and run within the area mom had marked out for them and all appeared to be having a great time.
Personally I would spend a good part of that 3 hours on the move since they will have been on a plane and have to get back on a plane again...wear them out!! And the nice part is you can walk for miles in the Atlanta airport...even without crossing the security gate...there is lots to look at and you can hype it up before arrival as part of the adventure!!