The "Unofficial Guide" thread has a link to a discussion about business class seat selection strategies, and in there you can find some information about upper deck versus lower deck. It's an issue that people have debated for nearly 40 years, and certainly it will continue with the two deck A380 entering service soon.

The answer is highly situational and depends on your personal preferences. In my situation I tend to select main deck center aisle seating, because I stand the best chance of having the most elbow room (middle seat unoccupied) and not having to get up to let a passenger in or out of the aisle. However, if there are no aisle seats available, then I prefer the upper deck window seat because it has a side bin that provides some additional space.

If the flight is relatively empty I'll probably opt for an upper deck aisle seat, then enjoy the view from the window seat after pushback. If the flight is even emptier I'll opt for a main deck center section aisle seat then enjoy the view and/or try to rest as best I can by lifting the armrests and lying down across the seats. (It doesn't work very well, but it's better than nothing.)

Exit row seating sometimes factors into the calculus. The upper deck exit row is quite nice, and the window seat in that row is just as useful as the aisle seat for entry/egress.

Upper deck bin space is rather limited, but on many flights there's a closet. Lavatory access may be marginally better from the upper deck. Safety is better on the lower deck (no falling down stairs).