1)BinFolder:

in website bin Folder Dosenot Exits;
in WebApplication Bin Folder Exists;

2)SolutionFile

There Will Be NO solutionfile;
 in WebApplication exists solution file;

3)AddingClasses
When We Add A class to Website in should be App_CodeFolder;there will be NoNamespace will Exist by default;
in WebApplication When We Add Class To there will be NameSpace to The Class By Default;

4)  Deployement:
when Website is posted to the server the eniter folder and all sources files should be posted;
when webApplication is Posted to the server one .dll or single Assemblu is posted to the server