I use DevonThink Pro as my reference storage system. It is a document manager that allows you to organize your documents by folders, tags, or content.
It has a unique algorithm that allows me to find similar or related documents based on the text. For example, if I click on a a PDF that talks about Greek mythology, it will find similar documents in my database that talks about mythology (such as Egyptian mythology) or Greek history.
I have separate databases for different things. I have a database for each project or area of focus.
I can go to Safari and browse various articles that may be of interest to me. DevonThink puts a small icon on the toolbar. It quickly archives the current web page to my DevonThink database inbox for me to process later.
When I need to link a DevonThink item to OmniFocus, I can control-click or right-click on a document inside DevonThink Office and select "Copy Item Link". This copies the URL or path to the highlighted file(s). Then I can go to OmniFocus, expand the note and paste the item link. Whenever I look at OmniFocus, I know that I can just click on that link and it will launch DevonThink and open that particular file.
http://www.devontechnologies.com/pro.../overview.html
I try not to use OmniFocus as the catch-all for everything. My tasks go into OmniFocus. My brainstorming goes into my mind map program NovaMind. My shopping list goes to OmniOutliner. My calendar events goes into BusyCal. My contacts goes into Apple Address Book.