Create a dedicated folder at the beginning of your project. Throw everything related to it in there (Footage as well as Audition, Premiere & After Effect project sessions) when you start and you won't have to search through so many broken links.
That's what I'm doing... now. But I need to archive what I was doing last year, when I hadn't figured out the organizing.
From what I can tell, there's no way to archive much of anything from Encore, even in CS5. True? I'd really like to archive some of those menus -- I have no idea at all how to recreate them if I loose them.
What are best practices for archiving the whole thing?
I create a folder named appropriately. Inside that folder I have three more folders - Files, Audio and DVD.
Every audio file in use, regardless of which program I'm using it in, goes in the Audio folder (before I import it, that's key). When I'm ready to create the DVD or Blu-ray, that obviously goes into the DVD folder.
Everything else (except media and Cache) goes into the Files folder - PP project files, AE project files, images, everything. (And it goes here before import, again that's key).
When you're done, you have one folder with everything in it - except media and cache - for very simple backup to hard drive, data DVD, etc.