Overlay network are being widely used in various applications, the most popular ones that we know are Skype, Napster, KAzaa, Bittorrent. A cool application that I came across recently is the program called Localhost. It is a program that lets you access a shared, world-wide file system through your web browser. This file system is maintained in a fully decentralized way by all of the computers running Localhost. The program uses BitTorrent technology, and new DHT called Kademlia.
The previous interesting application that I posted about was feedtree which uses an Overlay(p2p) network called Pastry (a P2P network from academia, developed at Rice) & delivers a realtime RSS feed to the nodes.