I use a simple key/value configuration table for site wide things such as webmaster email addresses. I find it hard to imagine site wide configuration data with a more complicated structure than key/value pairs that shouldn't be in a specific table of its own. Can you give examples of the sort of site wide configuration data that is problematic?

If the configuration data only applies to part of the site it should be handled by the code that manages that part of the site and should either store the configuration in existing relevant tables, or should add configuration tables specific to the site area as required. It may be useful to write a base class that does most of the common heavy lifting for managing configuration data then provide site area specific derived classes as required.