1) Using technologies like (JSP,HTML,XML,Servlet,JavaBeans ,ibatis,struts) can we create applications which do not run in Internet explorer ( I mean other than web based application)
I'm not quite sure what you're asking, but -having an SCJP- you're obviously aware that Java can be used to create desktop apps, as well as web services, server apps without a GUI, and so on. JSP, servlets, HTML and Struts are used to create web apps, though.
By the reference to IE, do you mean creating web apps that do not run in other browsers, like if you're using ActiveX controls and such? If so, I'd advise to stay away from those; they negate a large part of the benefits of web apps.
2) Does PHP provide functionality like of Servlet, JavaBeans, JNDI and other Java based technologies.
Yes and No. There may be libraries and/or built-in functionalities that accomplish some of the same things, but PHP should only be used as the front-most layer of a web app; anything to do with application logic should be coded elsewhere.