[wwwald]

Bit late to this party, but I've been using WikidPad(http://wikidpad.sourceforge.net/) for years. It's OneNote for geeks.

Less capable of rich multi-media than OneNote, altough it handles basics like images perfectly.

LaTeX plugin for math.

Python-based, and easily hackable or extendable with plugins. Oh, and, open source (https://github.com/WikidPad/WikidPad/).

File format is based on SQLite with plain text files, so perfectly compatible with version control, and you'll never lose access to your content.