As EnglishBob refers, it is impossible to amass a huge library and be able to know exactly where everything is without any structure of organization.  There is content that you will never use or ever find.  It would seem prudent to start documenting what you already have through some type of organized database with images of the product, name, author, etc, then separate the contents by category.  Delete the items you don't need if you have the zips or installers stored elsewhere.  Only install files you will use for a particular project and once done delete them or transfer to CD or external HD.  I have set up such a system of my own and it keeps the runtimes trim and lean.  Only the most important files are permanently installed. 

Unfortunately for you, this is going to take years of dedicated overhauling to get your runtime respectable.