There are two tools that I really like -- Zotero does a great job of organizing references, keeping related things together, and has a decent search capability.

There are two tools that I really like -- Zotero does a great job of organizing references, keeping related things together, and has a decent search capability. The target audience is academia, but it works just as well for other kinds of use cases. I also keep a personal wiki running on my laptop to take down notes and organize my thoughts. I've tried a bunch of them and Confluence from Atlassian is my favorite. It has the ability to embed all kinds of different media and it's $10. Xwiki is pretty good too. edit: bad grammar :)