Well, Web application is a website (ASP, ASPX, PHP) and will always be viewed through web browser. Windows application is mostly an exe-file for example MS Word, Notepad and these applications run "standalone".
Web application is like a website and use for globally,world wide web,and different browsers but window application are use for one system.There are need to IIS server to run web application but no need any server for window application.
Windows application is generally a .Exe file and used for a limited users of the particular organization.Where as Web application is viewed using web browsers and it is available across the Globe.
Windows application will reside and be installed on a Windows Machine. Every new/different machine would need this application installed in order to be used. Web application would reside and be installed on a server(connected to network) and can be accessed from any machine connected to the same network without installing anything. Network can also be internet or local intranet or VPN.