After searching, I found a copy of WikidPad using .paf, but when installing it, it seemed to be rather shady - it wanted administrator rights, while the regular WikidPad does not require them. This is an open-source program, and if anyone would be willing to cut the installer, make a spashscreen and turn it into a .paf, I would be really appreciative.
License: Open Source
Description: Basically, it's a wiki on a USB stick.
I am not exactly sure how to test registry entries, so I don't have information on information written to the hard drive. However, it is listed on Wikipedia's page of portable software.