I'm specificly interested in why most of the (german) regions being splitted in a upper and lower part (e.g. Oberbayern, Niederbayern -> Upper and Lower Bavaria) are named opposite to their directions on the map. Sanity tells me the northern part should be called upper (...) and the southern part lower (...). So where does this naming tradition come from?
The names are older than the convention of putting north at the top of maps (~1500s). The convention is that the 'upper' places were higher up and/or farther up a river (which is generally the same thing as rivers don't go uphill). The alps are in the south and rivers flow north in Germany. For instance the Rhine is divided into the Niederrhein (lower), Mittelrhein (middle), Oberrhein (upper) and Hochrhein (high) parts.
Oberbayern is farther up the rivers (e.g. Inn) from Niederbayern. Lower Austria is not north but east of Upper Austria, but farther down the Danube. Both are upstream of Upper Hungary, and so on.