I use "OneNote". Yup.. its M$, but I am kind of a documentation guy... and I constantly make changes to customer networks via our internal projects and tickets, which requires organizing 20 some different customers that we support, and I can always pick up where i left off. My recommendation is that you locate the OneNote Store on a TrueCrypt Volume or similar.

Have your IT guys evaluate TrueCrypt. I've been using it for some time, and have collegues using it as well, without a negative experience to report.