Lots of good comments (and some not so good).
I'd like to clear up a few misconceptions I noticed going through the 50 pages.
It was posted that the Rolls Royce engine control (in the BA Heathrow accident) and the PW4000 engine control are both made by Goodrich (the implication that they both might have the same s/w error) Not true - the Trent 800 engine control was done by Lucas - now part of Goodrich. The PW4000 engine controls were done by Hamilton Standard (now Hamilton Sundstrand).
I was involved in the BA Heathrow investigation - there was a huge amount of data from the QAR and Flight Data Recorders - the fuel metering valves on both engines were commanded to open, the position feedback indicated the metering valves opened, but the fuel flow didn't increase. The only way that could happen was if the fuel flow was obstructed upstream of the fuel control.
The 777 'pressure vessel' is pretty much all aluminum (aside of course from the windows) - the main deck floor is largely composite, as is the vertical tail. As to how the 787 might hold up in a similar accident - the FAA had concerns regarding how a composite fuselage would hold up. They made Boeing do 'drop tests' of fuselage barrel sections to show they provided crash protection equivalent to an aluminum structure. Of course, we won't really know how a 787 will hold up in a similar crash until a 787 is involved in a similar crash - hopefully we'll be waiting a long, long time for that to happen.
While there is always risk that pilots will become too dependent on the technology, it's hard to argue with the results. Each generation of new airplanes has gotten safer - with the 777 arguably the best so far (A380, 787, and 747-8 haven't been out there long enough to be statistically significant). But this crash, along with the Air France A330, show that we still need to train pilots to fly, not just manage, the airplane.