Techniques are described for identifying the use of software applications, such as to determine an identity of a user interacting with a Web site or other electronic information service based on information regarding an application copy used by the user. When a communication is received from a software application, the communication is analyzed to attempt to identify a particular software application copy that sent the communication. Various types of information about a client software application copy may be used in the analysis, including information about particular configuration settings for the client software application and for the client computing device on which the client software application is executing. After a matching software application copy is identified for a received communication, possible inappropriate activities related to the received communication may be identified in various ways, including based on previous communications received from the same software application copy.