In my recent RCP app some unwanted preferences, contributed from other plugins showed up:
To remove them, just add the following code to your WorkbenchAdvisor class:
public void postStartup(){
PreferenceManagerpm=PlatformUI.getWorkbench().getPreferenceManager();
pm.remove( "org.eclipse.help.ui.browsersPreferencePage" ); //remove single contribution
pm.removeAll(); //just remove all
}