An application virtualization system enables server applications, such as web applications to be easily deployable, separates an application and its state from the system, and allows applications to be easily moved to another server. The application virtualization system provides a way to isolate conflicts and allow multiple applications that provide conflicting information to run independently and avoid conflicts. The application virtualization system receives notification of an application preparation session and monitors the session to collect configuration information that the application uses to run on a client. The application virtualization system stores the collected information until the application to be virtualized is deployed. When an administrator later deploys the application, the system retrieves the stored information and uses the information and information from the client to reconstitute the metadata and virtualize the application.