Best note-taking: Notability
Taking notes is a very personal activity, and dozens of apps for the iPad reflect those preferences. But two such apps work well for most people. One is the iPad's built-in Notes app, which is great for typing in text-only notes and having them instantly available to your computer and other devices via IMAP, Exchange, and/or iCloud syncing.
If you want notes that include audio recordings and drawings (alas, no syncing), get Notability. It's straightforward to use and can associate your recordings to what you type as you type; to hear the portion of a recording made when you typed in specific text, just tap that text.