At a minimum you should be check-in the .project and .classpath files. If anybody on your team is hard-coding an external JAR location in the .classpath you should put them up against the wall and shoot them. I use Maven to manage my dependencies but if you are not using maven you should create user libraries for your external JARs with with a consistent naming convention.
After that you need to consider things on a plug-in by plug-in basis. For example I work with Spring so I always check-in the .springBeans and likewise for CheckStyle I always check-in the .checkstyle project.
It gets a bit trickier when it comes to the configuration in the .settings folder but I generally check-in the following if I change the default settings for my project and want them shared with the rest of the team:
- .settings/org.eclipse.jdt.ui.prefs – it contains the settings for the import ordering
- .settings/org.eclipse.jdt.core.prefs – it contains the settings for the compiler version
In general I haven’t noticed Ganymede modifying files without me modifying the project preferences.