An online (and free) wiki encyclopedia is a tool that I find very useful in organizing references, and efficiently organizing the enormous amount of data a history researcher comes across and needs to keep track of.
Personally, I have created a private encyclopedia with pbwiki.com.
Very easily, I can create individual pages on various subjects, with links to other pages and to internet pages, a great way to deal with the complex interactions between references, topics, etc.
I can also organize these pages in folders by topic.
As an example, consider that you create pages on historical events, pages on locations, and pages on historical heroes… Each time that you mention a person or a location as you discuss an event, you can link your event page to a corresponding location or person’s page… or to any online reference, photo, etc…
There are a number of free softwares online to build your wiki, but PbWiki (they called it PbWiki as in peanut butter, for you to easily remember the name) has great functionality and a very user-friendly interface, in my opinion.