Web based application: Application will be loaded in the server. Client machine use the application using URL. You have to test it on different web browsers. Web application is tested mainly for browser compatibility and operating system compatibility, error handling, static pages, backend testing and load testing. It works on 3 tier architecture.

Window based application: runs on personal computers and work stations, so when you test the desktop application you are focusing on a specific environment.You are focusing on a specific environment  It works on 2 tier architecture.