I did a quick search but didn't find what I was looking for. So feel free to flame me if it's been posted before. Just ease the burn a little with a link or better query for searching.

One of the things mentioned on Hacking Dojo (in one of the classes), was using a personal / desktop wiki to keep track of your notes when doing pen tests. Thinking about it, I think that's a better idea for any long term tracking (been doing it via text files but find them lacking). I asked on the Hacking Dojo student forum, but figured I'd ask here too.

Does anyone have recommendations for personal documentation / project documentation / pen-test documentation?

I've used Leo, and Twiki in the past. Some have mentioned TiddlyWiki, but I  want something more than a flat file (Why I'm not firing Twiki back up). I've also been looking at Zim, but not sure about it yet.

Might be overkill depending on circumstance, but I have a personal server running dokuwiki.

Works perfectly for me needs and can access from anywhere. Plus if/when you need to collaborate/expand just allow another access and all previous info can be shared.

That's a really good idea - whomever said that is a genius!  

I use an iPad now for my wiki - portable, and powerful. The app I use is "Trunk Notes" - I can also serve up the wiki data via wi-fi in case I want to copy it off easily. It can also sync with dropbox if you want. Here's the info:

http://itunes.apple.com/us/app/trunk-notes-note-taking-personal/id302880785?mt=8

It really was a great idea, thanks for it.   I've spent several hours at work (ok almost all day yesterday, and half the day today) setting my personal wiki with Zim.

Not owning anything from apple newer than an Ipod Color that doesn't do much for me. But  I have multiple Linux based boxes (and Zim is cross platform). Only thing I already know is going to hurt me with Zim is the sharing bit.