Everybody's always trying to make a better note-taking and organizing tool. After all, a lot of what we deal with in life is little bits and pieces of information. When the back of an envelope can't serve any more as your note-taking platform of choice, there is no end of little notepad apps and big deal outliners that are available for you to use.
MindRaider is a personal notebook and outliner. Instead of keeping several different lists of the stuff you need to take care of—including the inevitable list of the lists you are tracking—just stick it all in MindRaider. Enter your notes, important URLs, and more, with whatever annotations will help you to better remember and understand what you're talking about. Once entered, you can locate your information by drilling down through the outline structure or by using its robust search functionality. It supports several different views, which can help you to organize your data, as well as learn about relationships between different elements.
MindRaider is a free download. It's available for Linux and Windows, as well as a Java version, making it Mac-friendly as well.