The F135 STOVL propulsion system weighs almost 4,000 lb more than the CTOL version. I would guess that this number includes only the bits for which P&W as prime is responsible, which would not include doors and actuators.
The difference in OEW is less, as Engines correctly points out, but that is due to the omission of the gun and its feed system and an aggressively lightened airframe.
As for the F-35C: It was the last version to close and the wing area and OEW continued to grow through 2006. 35 per cent bigger wing than a Super Hornet, because it lacks an effective high-lift system. I don't think it's a great example of a CV penalty at work.
On the Rafale commonality: I don't have any parts-count numbers, but I do know that Dassault employed and improved CATIA with the aim of getting the best balance between eliminating "scar weight" on the CTOL and maintaining commonality. Some of this involved the idea of "cousin parts" - differing in weight and strength but fitting together in the same way - and the idea of concentrating the difference in the smallest possible number of parts. This was a JSF goal but I think a lot of it went out of the window in the Great Weight Panic.
