I recently discovered org-mode. Honestly, it is by far the best note-taking application I've ever used, especially in any math-heavy field, since it supports cross-references and most math symbols. And unlike LaTeX which ends up filled with markup, org stays very clean. However the basic export (to HTML and pdf) is not that good.
There's also support for basic spreadsheeting, but it gets very slow as soon as you have more than a couple hundred rows with auto-computed column values.
Sample look and feel of one of my notebooks: http://i.imgur.com/SZTxQ6v.png