I have a similar system for a lab notebook / to do list, but without encryption. I use a light weight wiki, Zim http://zim-wiki.org, and setup the directory in my Dropbox folder. That way I'm able to use the full wiki on my desktop, laptop, and work desktop. Because the pages are plaintext with simple wiki markup, I can also view and edit them on my phone.

Zim is also nice for me in supporting LaTeX equations (via a plugin) and being written in Python, I've made a couple of custom tweeks.