PersonalBrain is a full-featured mind-mapping program, designed to create a "digital home for your mind" that can help you visually organize almost any sort of process or project as a dynamic, interconnected system of Thoughts (called a Brain). PersonalBrain gives you a fairly intuitive interface for collecting, organizing, viewing, and navigating ideas, tasks, Web sites, related documents, and more.
Whether you're building a complex Web site or conducting academic research, this app can help you build searchable networks of information with tools for taking notes, creating shortcuts (pins), zooming out to get a higher-level view of your Brain (with "Distant Thoughts" and Outline views), and even generating reports. WebBrain publishing lets you sync a Brain between multiple machines, or upload a version for fellow collaborators to see. A new Transparent mode also lets you view a Brain directly on top of any other application without obscuring it, for a futuristic HUD vibe--and a related Mini mode makes it easy to keep a floating search box handy. PersonalBrain also has nice extras like a global system of tags and types, a calendar that can sync with Google Calendars, a full-screen Presentation Mode, support for HTML export, and integration with Outlook as well as Spotlight, QuickLook, and core Mac apps like Address Book.
Personal preference can be especially finicky for this sort of software, so definitely try before you buy and check out the app's user guide and tutorials (and even weekly Web trainings). PersonalBrain offers a 30-day trial of its Pro version, although a cheaper Core and much more lightweight Free version are also available.