People seem to believe that turning a bike upside down is an inversion of the natural world order, and worse, the pezzazz will dribble out of the bottom bracket to the saddle, giving you lumbago of the sit bones, and consequently neither you nor the bike will ever feel quite right ever again. Despite this superstition, as an atheist, I find little evidence to support this surprisingly widespread theory.
However, washing your bike upside down will tend to make your saddle mucky. Easily remediable, though. Removing and replacing wheels, though, on an upside-down bike is simply the easiest, gravity-aided procedure - the damn things just want to drop back into position. This though is highly frowned upon, as roadies roll past, sympathetically mourning your lost pezzazz, as you mend your roadside puncture.
In other words, do what feels right to you.