In my book, I recommend that, whenever you start a new project, you open a new folder/directory and save your project files and media files in it. This makes removing all of the project, media, temp as render files when your project is done as simple as deleting the folder.
Once you've got a finished project, there's no need to save your media or project files. You just won't be able to re-open the project later an re-tinker with it.
Read Bill Hunt on project setup http://forums.adobe.com/thread/919388?tstart=0
If you think you will ever want to go back to a project, just move the entire folder/sub-folder to a USB drive for storage
Steve's approach works well for me as long as I remember that step two after starting a new project is to make sure all the "scratch disks" are set to "same as projects". All but one setting will remember "same as project", but a single setting remembers the last project -- which may be a small "bug".
I find Bill Hunt's recipe is too complex for small "armature" or "home user" projects. I find one folder, without the subfolders, sufficient.
It all depends on the intricacy of one's Projects. If I only had a single Video file, and no Still Images, Music, or SFX files, and no Titles built in PS, then it would be too involved. However, most of my Projects ARE intricate, so keeping things separate is important to me.
Definitely like the usb drive idea. I mainly want to keep the source shots. You never know when you might think of a shot that you could use for something else and having it somewhere physical and not taking up space on the machine is great. The only thing I hoard are my music collection, various memorobilia from my band and such, original recordings from my band and now I can start a collection of jump drives that could fit in a jar. Cool, thanks!
I do the same thing. My original Assets (Video, Audio, Stills, Titles, etc.) are kept on my NAS, and when needed, I just Copy those to my internal HDD, for use in a Project.
As you say, you never know when you will need something from a previous Project.
I am also always shooting "stock" material, thinking that it might be useful later, like traffic in London, horse-drawn carriages in New Orleans, tourist buses in Washington, DC - whatever.