For note taking I use the open sourced Notational Velocity [1] (actually I use nvAlt [2] which is a fork that has some extra features like Markdown support). My two favorite features are that it can store your notes as plain text files in a folder of your choice, plus there's syncing through Dropbox or Simplenote. Notational Velocity is a Mac app, but with Simplenote you get x-platform support.
[1] http://notational.net/
[2] http://brettterpstra.com/projects/nvalt/