Some very knowledgeable people swear by wikis as personal organizers. They work with any OS, they're easy to organize, and they make it simple to link related information in an understandable way. With TiddlyDu2, you can painlessly turn a wiki -- a Tiddlywiki, specifically -- into your own organization system.

You can either work with your wiki online or download it for offline use. TiddlyDu includes important features like integrated goals, projects and tasks that can quickly be associated with your contacts and calendar. Basically, it's whatever you make of it. There's a full Tiddlywiki tutorial available, but it should be fairly intuitive to learn TiddlyDu2 if you've used another wiki before. Download the .html file and start messing around until you get your wiki (and your to-do list) organized.

UPDATE: Dave Gifford points out that there's actually a newer version, TiddlyDu3, so check that out first.