I have searched a lot about the difference between Website and WebApplication but didn\'t get a clear cut answer.
Even I am more confused a
A web application will have some dynamic logic behind it (i.e. do something). Normally it would have a database and some server side programming language to power it.
A website can be completely static - for example just a bunch html pages linked together.
A website could also be a collection of web applications and static pages.
Update:
If you are talking about the difference between visual studio web application projects and web site projects, read this article and this one.
Web application projects have a project file and can be compiled to a single binary (plus .aspx pages and static content).