After spending 99% of my time fiddling w/ my outlook and palm add ins, and 1% using "Getting Things Done," I pulled everything off of Outlook and my Palm and I'm doing a plain vanilla implementation.
I keep projects tied together by just adding an arbitrary number like "(P5)" to items (tasks, notes, etc.) so I can link them together.
I use the standard categories for Tasks (@home, etc.). I have one called Projects where I list the projects I'm working on, with the body having the project summary (deliverables, risks, vision, etc.)
I'm using notes to track all my projects, with either unordered lists or tabbed pseduo-outlines.