I am trying to develop new website in spring/hibernate/tomcat/JTOM.
I am just using those jars and not modifying their source code.
Do I need to make my website also open source?
what are the things I have to take care in terms of licensing.
Start by reading the licenses of all the libraries you intend to use. I *think* all the ones you mention don't require you to open source your entire site (the one I'm not sure is JTOM, with which I'm not familier). Very few licenses require open sourcing of a web site's code when used as part of a web app; the GNU Affero license is a notable exception. You need to avoid libraries that use those in a business setting.