First I must say – I came a long way before started developing for web (I was mostly C++ and system level developer), this is why my opinion might not be very balanced.
Lets be honest – there is no exact definition of what web application means and how is it different from regular website. But during this article I will concentrate on applications requiring frequent user interaction (e.g. management systems, editors, remote control, user collaboration, etc.). If you are about to develop mostly content delivery application (e.g. catalogs, posts, galleries), use PHP without thinking twice – this article is not for you.