good premise
I have noticed - anecdotally, informally - a similar pattern. For an local angle - for you at least - add to the list the Qantas 747 overrun at BKK sometime in the 90s, aircraft very badly damaged (repair bill exceeded write-off value but QF chose to maintain their record of no jet hull losses - again, anecdotally). FO (who was flying)'s wife was in the jumpseat. And they really screwed it up, hot on approach, only retarded three engines on flare and roll out, failed to use reverse thrust on a wet runway etc.
The new standard bearer for the phenomenon is the Aria Il62 crash in Mashhad Iran July 24 09 totally due to supernumary crew on the flight deck, a four-man deadheading crew in addition to four (inc radio man) operating crew, some presumably standing and all with a different opinion, so it was perhaps inevitable that they would cross threshold at 200mph, touch down in the second half of the runway, and end up 2km (yes) off the end, with all eight pilots plus another nine (cabin crew, sky marshall, three or four pax) killed. Very tragic (the entire Il62 team in Iran wiped out) but utterly avoidable. It almost transcends the issue of jumpseaters and enters Darwin Award territory.
Same goes for the much documented accident that befell an Aeroflot A310 en route from HKG to Moscow, when the captain put his 15 yo son in the left hand seat, who unwittingly disconnected the autopilot in the roll mode and what transpired in the ensuing final minutes I will leave for you to read up on. A great Aussie book, one of McArthur Job's series of four in-depth volumes on individual accidents, covers the Aeroflot disaster in great detail.
Finally, and more of a cockpit invasion than a jumpseat issue (but relevant to a locked cockpit door policy), a mentally disturbed passenger burst into to the cockpit of a pre-9/11 BA 747 en route to Nairobi and grabbed the controls, aircraft lost 16,000 feet (iirc) before the guy was ejected back into the upper deck passenger area (and the arms of Roxy Music singer Bryan Ferry). There's a few of these, didn't an ANA 747 get within mere hundreds of feet above the water at the hands of a knife-wielding MS flight sim nut?
Where does that FedEx guy who went bananas fall? Cockpit invasion or jumpseat hazard? He was FedEx crew and (under slightly false pretenses, he had been suspended from duty) in the jumpseat from boarding onwards.
Oh one more - the worst landing I've ever experienced was on a Ryanair 737-200, after a flight where all the PAs made mention of the two captains (as opposed to a Capt and an FO) up front. Poor shock absorbers never knew what hit em!
On a personal note, in all my experience without exception, responsible jumpseaters add more than they detract from the cockpit, contributing an extra pair of eyes at busy times (but silent like mouse) and a welcome source of entertainment ("I am here to entertain - and inform.") during quiet times.