I used to run a wiki (instiki) on my local machine to do something like this, but I eventually gave up reinstalling it on new machines after running into problems with data compatibility (unlike Zip, it isn't stored in plain text files).

Now I just use a plain text file for my todo list, and either google docs or drafts in gmail for my various personal notes; I'm not extremely satisfied with it either - Google docs is convenient for access from anywhere, and it's nice to be able to use spreadsheets, but I miss the ability to easily create many small interlinked pages.

Do you use Zim on several machines, synching the text files from one to another with source control?