I have settings options all over the place! Some are now even showing under Applications> Special. They look like KDE things.
Sounds more like a problem on the kde side to ensure that the settings have suitable categories in their desktop files.
Can you be more specific on the names of the programs. On my Rawhide system I have no Applications > Special category. Screen shot might help track down what they are.
If I understood the problem report properly, the problem is that they are KDE System Settings (formerly KControl) modules (KCMs) and that they're showing up in the GNOME menu as applications which makes no sense. These things should be hidden already! Maybe they also need an OnlyShowIn=KDE? There are KCMs in a few KDE modules (kdelibs, kdebase-runtime, kdebase, kdebase-workspace, maybe others), so I'm not sure which ones are the exact offenders there.
Changing version to '9' as part of upcoming Fedora 9 GA. More information and reason for this action is here: http://fedoraproject.org/wiki/BugZappers/HouseKeeping
Is this still an issue?
Should be fixed in recent kdelibs3,kdebase3 updates. Feel free to reopen if anyone experiences otherwise.