1, Workflowy - It took me a while to warm up to this one, but with the addition of an iPad and iPhone, being able to outline anywhere, at all times, sold me on it. It has weaknesses (can't multiple select items, for instance), but overall it reminds of BrainStorm or Ecco. It's technically not a desktop app, but it does have offline access, and I find its speed to be equal or better to most desktop apps.

2. Evernote - Digital junk drawer.

3. Notepad++ - Programming and general text editing.