There are many decent notetaking programs for Linux, including NoteCase, KnowIt, BasKet, Wyneken and others; other solutions such as a wiki, text-file, Tomboy notes, or sticky notes can be used. However, none of them are built specifically for educational use, and it would greatly increase the productivity of students to have an information manager that was.

Most note-taking programs currently have a sidebar on the left which contains a hierarchical note tree. I believe that this outlining model is actually unnecessary for students, and I find that I tend to just have top-level notes for each of my classes and then a flat sequential collection of notes for each class one level below. It would be better to have the program store a flat series of notes for each class, get rid of or make temporarily viewable the sidebar, and have buttons for each class aligned horizontally at the top of the editor. For students, I think doing away with the tree structure of notebooks is a good tradeoff for the added simplicity and space in the UI. Notes could be scrolled through chronologically using back and forward buttons, and they could be renamed or re-ordered with a preferences dialog rather than in a tree view. Notes could automatically be named by date (this is similar to how Wyneken currently operates), or a name could be prompted for upon creation.

The ideal notetaking software for students needs to be WYSIWYG and, importantly, have a way of making bulleted lists that does not require any clicks (perhaps with a keyboard shortcut or by recognizing the “*” character as a bullet).

Task management programs such as Tasque and gtodo have the same problem of not being designed for student use and so being less than ideally useful. To enhance usability for a student, task programs should know what homework assignments and larger projects are. They should also get rid of almost all the manual preference setting required, and have the student only need to enter a title, optional description, and optional due-date, and select a class for each task.

The notebook and task list for each class could then be shown side-by-side in one application.

UPDATE: In September 2008, I discovered TakeNote, which is almost the ideal notetaking application – it does what you want it to do and nothing more.  However, I later switched to Zim Desktop Wiki, which is fairly popular in the Linux world, because it seems a little more polished and its linking ability could be useful.

Organization

Like any bibliographic database tool, Zotero easily records publication information about sources. Automatic recognition of sources on web pages through COiNS and other metadata is excellent. Organization of sources is very intuitive and easy. You create collections of sources, which can have subcollections as well. Multiple items that are part of the same source, for example a book source record and a link to a web page containing an excerpt of the book’s text, can be bundled together collapsibly under the main source record. The My Library view shows sources from all collections in a flat view. The organizational structure works very well, but, unfortunately, when it comes to exporting sources to a bibliography, there is no option to include items in subfolders, so you must go into the My Library view and select the sources you want to export.

Store copies of web pages and files

Probably the single best feature of Zotero is its ability to store copies of your sources. Rather than having to keep track of an HTML or PDF file saved on your hard-drive, you can simply take a snapshot of a web page, and Zotero stores a copy locally, which you can later view without having to worry about where you kept it (or if you’re offline). You can also attach any file type to a source record and Zotero will store a copy of that file. This is a helpful feature that gets rid of a lot of manual organization normally involved in research.

Notes and Annotation

You can create plain-text notes (basic formatting would be a welcome addition), either attached to sources or standalone. Notes, along with snapshots and PDFs (if you have PDF-to-text software installed), are full-text indexed by Zotero for searching. Sources and notes can also be tagged and linked to related items.

Highlighting and annotation of saved snapshots is very simple. In order to highlight text, one must simply select it. Annotations, similar to sticky notes, are added with ease.

Exporting

Zotero can save selected sources as bibliography entries in many different styles, such as MLA, the Chicago Manual of Style’s style, and those of many journals (and more can be installed). These can be saved to RTF or HTML, printed, or copied to the clipboard. It can also export to many formats, including BibTex and, amazingly, Wikipedia {{Cite}} templates. An HTML report containing a summary of source bibliographic information and the full text of notes is also useful.

Microsoft Word and OpenOffice extensions place a toolbar in your word-processing program, from which you can select a source to cite (footnotes and endnotes are generally supported) or insert a bibliography. In my experience, the OpenOffice extension was slightly buggy, and messed up the usage of Ibid, but it was usable.

Zotero can also create a nifty timeline showing the distribution of your sources.

The next version of Zotero is planned to use a server where users can store their sources; if this were made social like del.icio.us, it would be another great development for the research process. Overall, Zotero is by far the easiest to use and most powerful (and certainly most suited for my needs) bibliography manager I have used.