Sounds like you need a commonplace book. I read about them in the book "Where good ideas come from". A commonplace book was a notebook used by the likes of Darwin to store and rehash ideas. I use what I consider to be the modern equivalent, which is a personal wiki (I like tiddlywiki, which is a self contained file I put in dropbox so it's available on all my computers. The author cited above uses software called devon-think, which has the advantage of including semantic search, which pairs ideas based on the words in them that you might not otherwise put together.

Typically when reading I record quotes and ideas and relevant reference information. The wiki allows tagging so the content gets a number of tags.

I've found the ability to re-discover thoughts and ideas to be extremely useful - and was glad to find that there is a historical precedent for this problem/solution.