Jarnal is an open-source application for notetaking, sketching, keeping a journal, making a presentation, annotating a document - including pdf - or collaborating using a stylus, mouse or keyboard. It is similar to Microsoft Windows Journal and to the earlier Mimeo whiteboarding and Palm notepad applications. There is also a commercial knockoff of Jarnal called PDF Annotator - for $50 you can enjoy a subset of the capabilities that Jarnal provides for free.
Why is this program better than Microsoft Windows Journal or One-Note? Because it is written in Java files can be edited and viewed on any platform, and the editor/viewer is freely redistributable - not to speak of customizable. MS Journal files can be edited only on a Tablet PC and viewed only with Windows XP or 2000. One-Note also uses proprietary file formats that can be viewed only on a few platforms, and edited only by purchasing the latest version of Microsoft Office. In Jarnal the files are in a standard non-proprietary format, human readable, and usable by other applications. By default, no information identifying the author is stored in the file. Jarnal also offers document annotation capabilities, collaboration and networking connectivity not available with the MS programs. [If you are interested in this software and run Linux, you should also take a look at Gournal and Xournal.] Why is this program better than PDF Annotator? Because it does for free everything PDF Annotator does and much more: cross-platform support; the ability to enter text from the keyboard; combine pdf documents and rearrange pages; the ability to annotate faxes and other non-pdf documents - to name a few.
I tried using this application and found the concept of collaborative note taking through Jarnal very exciting. It was easy to make one of the Jarnal instances into a server and Jarnal copies in other machines to connect to the server. Requires no installation and the menu options seem to be exhaustive - the signs of a mature software ;) The ability of annotating a pdf document is nifty. It basically means we can edit and save our changes made to a pdf file. A lot for very less by David K. Levine and Gunnar Teege.
Check out the Demos: There is a simple on-line demo and and a more advanced (and fun) demo demonstrating networked usage.