Isn't this sort of the original intent and purpose of Literate programming. I just spent a bunch of my time creating my emacs configuartion in org-mode using babel [0] and man, it was a cool experience. You can comment out the wazoo, linking to the web, other files or other parts of the same file all organized in a custom hierarchy or whatever you choose.

Then just C-c C-v t and all the source code is in a clean seperate file. You can even set it up to include the comments, link to the comments, or whatever other way you want the output to be. If I ever pursue programming more seriously, I can't image not seriously trying to do it in this manner.

0. http://orgmode.org/worg/org-contrib/babel/