1) Security system - Aftermarket
2) Cap - Aftermarket
3) Skid plate - Depends how tough you plan on being.
4) running boards - Have em, hate em, wouldn't have gotten them if I didn't like the rest of the truck. Although they do block a lot of debris from chipping the lower paint.
5) dimming mirror - Not for me since I always tint the windows, but I would get factory if I wanted it.