I use a wide variety of apps to take notes, but the majority of my notes end up in OneNote or Evernote. OneNote is best for rich notes that include a lot of content (college lecture notes especially), while Evernote is better for info snippets.

That said, my favorite tool for saving information is 37signals Backpack. I currently use the free version, which is nice but limiting, but upgrading is rather expensive. I'd love a self-hosted alternative that was cheaper if anyone has any ideas ... but it would need to work as nice as Backpack (drag and drop sections of pages is especially nice).