One use-case: at my last gig, we assigned each customer a new sub-domain, under our main one. Route 53 worked great for this. We used boto (python API for AWS) to create EC2 instances, get a static IP, and then create a new DNS entry in Route 53 to map to that IP, all in about 5 minutes.

Prior to Route 53, we used to do the mapping manually, as our primary DNS provider did not have an API.