Okay, here are some notes to remeber that I took out of the OFF209_SharePoint Governance and Information Architecture Guidance session presented by Joel Oleson and Shane Young.
The slides are attached to this post [:D]
Quotas: only apply to Site Collections. Do not apply to individual sites
Site Directory: do not use automtic listing of new sites. The reason for that is quite simple: the newly created sites are empty! So use the Approval workflow for adding new sites to the Site Directory after it has been reviewed for valid and usefull content.