"For ages scientific notebooks have been the mainstay of scientific research and have always had one thing in common: paper. Until now that was mostly due to a lack of options. Today as science and computers have become more and more inseparable the appeal of digital notebooks is quite clear. ''Digital notebooks have one huge advantage over their hand-written brethren - search capabilities.'' The ability to easily search for notes rather than paging through 3-ring binder after 3-ring binder is a HUGE timesaver. Digital notebooks do have their shortcomings, primarily the inability to easily write equations and draw diagrams. However, by adding LaTeX to the mix digital notebooks can handle equations with ease, and scanning in diagrams isn’t too much of a chore either. I’m going to assume some working knowledge of LaTeX, however, if you aren’t familiar with LaTeX don’t worry it isn’t required to use TiddlyWiki. Besides, typesetting simple equations in LaTex is actually very simple.

There are quite a few scientific notebook applications out there, but I recently found a solution that I think quite elegant and possibly the simplest to use. TiddlyWiki is a wiki platform not unlike MoinMoin and DokuWiki. TiddlyWiki has a few advantages over these other wiki solutions, however, primarily its portability and interoperability. TiddlyWiki consists of one simple html file which makes it extremely easy to take your notebook with you on a USB memory stick. In addition, since the only program required is a standard web browser (IE6, IE7, Firefox, etc) you can take notes anywhere there is a computer (no internet required). For example I can take notes from the lab machine running Windows just as easily as I can from my iMac at home."

From "TiddlyWiki and LaTeX - Scientific Notebooks Made Easy" by Franklin on October 10, 2007
Reposted on Nanowiki.