I installed Py Wiki on my laptop and I'm experimenting with using my Wiki as the Programmers Notebook. You can link things together, search etc. One problem is that you cannot doodle, like in a real notebook. -- Richie Bielak
You should be able to do this; make a real hyperlink to your favorite drawing tool, or to a file managed by that tool. Or find/write a Java drawing applet and incorporate that into your Wiki engine. Hmmm... sounds like an interesting concept for something to incorporate into Wiki Wiki Web or JWiki (see Java Wiki By Richard Keene)... -- Dan Hankins
I've added it to my set of Self User Stories for JWiki. -- Dan Hankins
Twiki Clone has a Java drawing applet plug-in available, based upon Hot Draw -- Kris Johnson
One big benefit of using a wiki as a notebook is that you can share it with others. It's nice when you jot down the description of some problem in the wiki, and a few minutes later someone says "Hey, I know how to fix that!" Or you can search other peoples' notes for similar issues. -- Kris Johnson
Another benefit of using a wiki as a programmer's notebook is Inter Wiki. You can link up your personal notebook with the company-wide wiki, or with the Wiki Wiki Web itself.
I have used an installation of twiki.org 
for this purpose. I use Visio and attach them "inline". It has a drawing plugin as well twiki.org -- Stanley Knutson
My Power Book runs an instance of Snip Snap for a notebook, and I'm looking to integrate my notebook and personal blog. Someday, I hope to figure out how to effectively host a shared "snip space" for all our developers, but I haven't figured out how to encourage sharing of knowledge while respecting territory (a Programmers Notebook is a very personal thing). -- Hans Gerwitz
We use pbwiki. We started with a Learn Log for each member of the team and Project Log for each project. It is still an experiment since the team is a set of interns. -- Dorai Thodla
I use tiddlywiki.com with Git for version control, so I can keep the wiki portable. -- Dafydd Crosby
See original on c2.com