Ivan Todorov of Blitz shared some of their guidelines on project directory structures and naming conventions on his blog. Its always very interesting to see how people organize their projects and they seem to have a very effective system going there. Also worth noting is his step-by-step guide on version control with SubVersion, I'm still using CVS for most projects but am seriously considering on finally making the switch mostly because of the more efficient storage of binaries which of course is very important as a Flash developer when working with FLA's.