File Structure & Organization

Hello!
How do you guys set up your files?
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We don't really have a system here.
There is a general layout for where part programs should go; locally, on the machine computer.
I recently saved everything to a server on site, because god forbid anything should happen to the desktop. (which died last week )

Now, I'd like to have some organization in there.

I deal with, mainly:
- CAD files, typically STEP and IGES.
- PDF files, typically blueprints
- PRG files

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I am mainly concerned with the PC-DMIS files, however obviously I will take suggestions on organizing the other files.
Essentially, how do you tell the difference between a good and a bad program? (e.g. one that is production ready vs. what is being worked on).

I have many programs in varying stages of development.
Some are fully working programs that check every feature, but are for example using operator comments instead of a form
Some programs are up to the point where they check every feature, but aren't dimensioned.
Some are barely half done, prone to crashes, don't fully check something, etc.

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What are some good techniques for keeping relevant files together? A CAD file, blueprint, and PRG for the same part, for example