Our SVN server has a flat folder of projects. So they look like so:
internal--system
client-
It works great, IMO. Directory structure on the servers is simply the domain name. For my development computer, I follow the naming convention of the SVN server. Don't try to stuff everything into different folders - a simple, consistent, prefix can do wonders for organization. For internal items, there isn't anything wrong with generic project names ("Time Manager" "Finance Manager") and such (so that the folders would be "internal-time-manager" and "internal-finance-manager" and so on).
