I point out the db diagram cause remember eZ Publish 3 is based on the use of persistent objects. I seem to remember seeing a much better diagram with relationships but where it exists escapes me atm.
I can't believe that Heath missed the doxygen API documentation :) http://pubsvn.ez.no/doxygen/trunk/html/index.html
(Mostly?) Anything with a database table will have eZPersistantObject as a parent http://pubsvn.ez.no/doxygen/trunk/html/classeZPersistentObject.html Understanding this class is a good place to start. Especially look at the definition method & understand function attributes. http://pubsvn.ez.no/doxygen/trunk/html/classeZPersistentObject.html#b507c40150f7f749a092ad0b7fcb5df5
If you are looking at the content module you'll want to look at
eZContentObject
http://pubsvn.ez.no/doxygen/trunk/html/classeZContentObject.html
eZContentObjectTreeNode (nodes) http://pubsvn.ez.no/doxygen/trunk/html/classeZContentObjectTreeNode.html
There isn't a lot of deep inheritance mostly alot of interlocking classes.