Is the application named exactly "System Preferences.app"? I believe the link in the apple menu has the path to that app hard coded, thus if it was renamed it wouldn't open.
I had the same problem long time ago ( more than an year I think). Don't remember how I fixed it. May be it was related to Mac OS installation on a second partition. Try the following:
1. If you have another OS X partition, unmount it and see what happens.
2. Try the usual stuff: repairing permissions with Disk Utility and reinstalling the last combo update.
3. (May be) Create archive of the System Preferences.app by control-clicking and selecting the respective contextual menu item. Delete the System Preferences.app and un-archive it from the previously created archive. This should update the application database in the OS (theory).
Comments
1. If you have another OS X partition, unmount it and see what happens.
2. Try the usual stuff: repairing permissions with Disk Utility and reinstalling the last combo update.
3. (May be) Create archive of the System Preferences.app by control-clicking and selecting the respective contextual menu item. Delete the System Preferences.app and un-archive it from the previously created archive. This should update the application database in the OS (theory).