Why not take a look at the open source projects out there.
Take a look at the source code, choose one or many of them and join the projects :-)
A few examples:
GVSig with both desktop GIS, mobile version and mini version for phones http://www.gvsig.org/web/home/gvsig-home/view?set_language=en
JTS, Java Topology Suite (I think it means) http://www.vividsolutions.com/jts/jtshome.htm
Another desktop GIS http://openjump.org/
GeoServer, generating web-mapping services (website seems to be down right now) http://geoserver.org
and so on....
Sextante might be of interest to you.
Here is some information from ESRI on how to develop GIS applications with Java:
For Java EE developers, Esri offers the Web ADF for the Java platform, a Java web framework that extends the JavaServer Faces (JSF) specification.
Geomajas is another open source project for building Java based web applications. It uses GWT to allow you to do everything in Java. There is a learning curve as it expects maven and spring knowledge, but it includes many goodies for your application (e.g. caching, printing,...) thanks to the many plug-ins.