As far as I know, it is not possible to load the jar files or set the CLASSPATH at runtime unless you have written your own class loader. Tomcat is a good illustration in which the tomcat's class loader loads the jar files dynamically in multi-level.
http://tomcat.apache.org/tomcat-6.0-doc/class-loader-howto.html
There is a common class loader which allow the jar files to be shared accross all web application. However, if you want to addthe jar files which are only loaded for the web application then you should add it under webroot, e.g. WEB-INF/lib. The libraries in this folder are not shared to all applications. For example, this means if two web applications are using different versions of the same library, they will not be mixed up.
Since I am using maven to manage the project, I do not need to worry about where to put my ja dependencies. Maven automatically bundles the libraries into war file for me.
So if you are not using servlet container, e.g. tomcat, jetty, etc. , then you will need to write a class loader. If that is necessary, then have a look into tomcat but it may not be easy.