I haven't seen one, so let's start a list right here.

- includes - include files with php functions and classes that make up the Drupal API
- misc - miscellaneous assets like javascript files and images
- modules - Drupal core modules (not meant for contrib and custom modules)
- profiles - installation profiles
- scripts - shell scripts for developers and administrators
- sites - all files that are added by a developer to create a site

 - sites/all/libraries - 3rd party libraries, eg. a wysiwyg editor
 - sites/all/modules - contributed and custom modules
 - sites/all/themes - contributed and custom (sub)themes
 - sites/default - contains the default settings.php
 - sites/default/files - the default directory for user-uploaded files
- themes - Drupal core themes