Japan Airlines have some of their international 747-400's fitted with economy class on the upper deck, and I have the chance to sample that twice (ship no. JA8075 and JA8078).
There were 10 rows of 6-abreast seating, plus washrooms and a galley. On both occasions I flew, only about 20 of those seats were occupied; and yet there were 2 flight attendents up there, so I guess you might say that we were well taken care of!! The atmosphere certainly felt more intimate than in the main deck. Felt like I was flying on a corporate jet, but with the smoothness and stability of a jumbo.
Like most others have observed, it was very very quiet up there. However, due to the curvature of the fuselage at the upper deck level, the windows are tilted at a considerable angle away from you; viewing the outside world is therefore less convenient.
All told, I'd say it's the best place to be to catch some sleep, especially when you have a long overnight flight ahead.