One big problem which I have with the skeleton I built is that the axes of the legs and the back are different which caused unwanted behaviour of the feet after the character was skinned. As I am building the bones of the legs downwards and the bones of the back upwards this happens automatically.
In the Blender 2.3 guide I found this comment :
"An easy way to automatically orient the z-axis handles of all selected bones is to press CTRL - N "
If I do this when the armature is in edit mode I get this line "recalc bone roll angles" which is not having an effect on the orientation of the axes.
Here You can have a look at the file with my bone system :