When you publish a Web Site, you will get multiple dll files like App_Web_ihlfp0qs.dll, App_Web_w7jvlmwm.dll etc. in the bin folder. If you publish the same appliation again you will get dlls with different name. However, if you publish a Web Application, you can compile the code to one dll with a static name. If you publish the Web Application again, the dll file name will not change.To my knowledge both are good to use.In order to give more security,usually some prefer WebSite rather than WebApplication