We just published our first version of a java connector for CKEditor V3.x
You can find it here: http://sourceforge.net/projects/jckconnector/
It allows you to integrate file browsing/linking in your java server application.
Technically it uses vaadin the webinterface to the user.
You can provide your own version of the file store and link store.
It's the alpha release with probably some security holes "included"