Preferences

Disable help preferences

Put the following code into your subclass of org.eclipse.ui.application.WorkbenchAdvisor, and it removes the "Help" group from RCP preference dialog:

public void postStartup() {
    PreferenceManager pm = PlatformUI.getWorkbench().getPreferenceManager( );
    pm.remove( "org.eclipse.help.ui.browsersPreferencePage" );
}

"org.eclipse.help.ui.browsersPreferencePage" is the ID for the preferences extension point.

Add Perspective preferences

Remark : to find plugin id preferences, select Window-->show view--> PDE Runtime--> Plugin Registry ..... and try to find what you are looking for .....
For example, for "Workbench preferences", have a look in fable.eclipse.ui.ide and extension org.eclipse.ui.preferencePages.: id="org.eclipse.ui.preferencePages.Workbench_"_

If you want to add only perspective (for example) preferences, add a preference extension in MANIFEST.XML :
id : org.eclipse.ui.preferencePages.Perspectives
_name:_perspective(fable)
_class:_org.eclipse.ui.internal.ide.dialogs.IDEPerspectivesPreferencePage

//Add : org.eclipse.ui.ide in your Dependencies

In ApplicationWorkBenchAdvisor :

public void postStartup() {
    PreferenceManager pm = PlatformUI.getWorkbench().getPreferenceManager( );

    pm.remove( ""org.eclipse.ui.preferencePages.Workbench"browsersPreferencePage" );
}

public String getInitialWindowPerspectiveId() {
    IPreferenceStore pref = Activator.getDefault().getPreferenceStore();
    String ret = pref.getDefaultString(IWorkbenchPreferenceConstants.DEFAULT_PERSPECTIVE_ID);
    ret=(ret==null || ret.equals(""))?"yourDefaultPerspectiveID":ret;
    return ret;
}//