Windows/Mac/Linux: MindRaider wants to be the place you stash all your sudden thoughts, organizational notes, and inter-connected ideas. That's because it offers links, visualisations, and other tools to help you make sense of it all.
From the outset, MindRaider, a Java app that can run on any system that supports Java, looks like a kind of multi-window outlining program. And it is, in a way, but the idea is to use it as an uber-outline. You can attach files to notes, or create symbolic links to local files. You can inter-link notes, documents, and outlines, use contextual tagging for an extra layer of finding something later, and use any of the pre-defined categories to segment out your ideas into broad containers. It supports a huge range of note formats, from simple text file to TWiki exports, and has a number of visualisations that help you kinetically wheel your thoughts around and pick what to fill out next.
Honestly? It's an application that would take more than just a glance and quick twiddle with to get comfortable and productive in. That sounds like a deal-breaker to most idealistic productivity minds, of course, but it looks like MindRaider can be pretty powerful, once you get your system rolling with it. If you do, offer up some help to your fellow readers (and at least one editor here) in the comments.
MindRaider is a free download, works wherever Java does.