My first jumpseat landing was on an JAL 747-400 in NRT... Won´t forget that either. The 747 was a great plane, for passengers mainly due to its shortcommings. If you used it for range, you could not use the full pax capacity, hence the space even in economy class was still quite OK. I really enjoyed the Qantas flights, no comparison to what airlines offer today on the long range flights.
Upper deck never really impressed me much, it is quite narrow and loud, mainly due to the supersonic airflow around parts of it. JAL had economy seating on the upper deck, unless when seated on the emergency exit row with a free middle seat (FRA-NRT-SYD, which was great) I was not impresed. View is not impressive either, due to the orientation of the windows, and the emergency exit row misses a window anyway. Only the extra storage below the windows is great.