For those who've made the switch to Premiere Pro CS6, or even those using one of the CS products such as Production Pro, try using Adobe Bridge as your project organizer. It has some really powerful file organization capabilities, aside from your own careful organization of your folders. There's a feature called Collections, which lets you take any number of files (not just video clips...graphics, audio, whatever) and assign them to a collection. It doesn't move anything around, or duplicate files, it just creates pointers to your "stuff", so that you can find everything in one place, no matter where it is. Using that, in addition to the metadata, labels, and keyword features, allows you to keep your finger on thousands of files, view them, play them back for review, and drag and drop them into the various Adobe software packages.
Joe Bourke
Owner/Creative Director
Bourke Media
http://www.bourkemedia.com