One I use all the time and the other has only recently been announced:
OmniOutliner (http://www.omnigroup.com/) is a great freeform outlining tool that has a considerable number of features. As a writer, I rely on outlines. Plus, I've heard of some utterly amazing uses of the tool.
OneNote (http://www.microsoft.com/office/onenote/overview.asp) sounds like an amazing notetaking app. The ability to freely place text, graphics, and audio sounds like exactly the note-taking app I've longed for. Boswell for the Mac sounds close, as does Tinderbox. If this app stores the data in some sort of XML-based document, I would buy it in a heartbeat. I sure hope it's available for the Mac.