I am a computer science graduate and want to learn web application development. I have learned HTML,CSS and JavaScript. I have knowledge of Oracle and medium knowledge of C++.

Now I want to learn a server side scripting language. I am really confused what language should I learn. Personally I want to learn Java because I have learned Java SE pretty well. But though Java is a powerful platform out there it seems it is not as popular as a scripting language like PHP (considering my second choice) or others.

What should I do now? If it is not Java then what language should I learn and what framework?

Why not learn the basics of Java/JSP first, and then decide whether you want to learn something like ASP.NET or PHP.

If you have an objective such as what type of work you are planning to do, an answer may be indicated. I agree with pritaeas, given that you are a CS graduate, learning Java/JSP will be a good project for you and be useful in business applications.
IMO, PHP should be very easy to pick up quickly after you have a good Java proficiency.