Where can I find a list of diseases and their incidence?
About diseases in general, that would concern the health dept. of the respective country government, and the govt. is the most probable source for such numbers. 

However, orpha.net has two reports with numbers concerning hereditary diseases, have a look at http://www.orpha.net/consor/cgi-bin/Education_Home.php?lng=EN#REPORT_RARE_DISEASES