I briefly skimmed over the posted comments. Most of the programms are quit well for notetaking, indeed. But notes may only be the beginning, depending on the classes you take.

Note taking on a computer in a chemistry or physics class can be hard if your professor uses more than formulas. Even formulas are for that matter a difficult issue, unless you memorized all latex notations and your typing speed is that of master.

The point I want to make, there is not one note taking technique or programm that fits ALL type of lectures / subjects perfectly.

Because of that paper is the best option, it's the most flexible.

Since this site is all about GTD let me tell you how I think you can modify GTD to meet the students needs.

1. Capture tool: This should be a writing pad. Each lecture you take start by adding meta data at the corner of your first note paper: data normally is date, page, course name/number and Session Number. At the end of the lecture you may want to use a stapler to have all notes of that one lecture behind your first page with all the meta data. Then take all these stapled papers out of your writing pad and put it into your "Inbox on the Go"

2. At home/ in the library take all your lecture notes out of the "Inbox on the Go" and put it into your Inbox.

3. Then you would proceed like you are used to in GTD: Work down the pile and actionize your notes.

4. Actions most likely for you are: reviewing, supplementary reading, homework, discussing, exam prep, filing.

Reviewing is you read your notes. What have you not understood? What do you need to review further using books or trustfull internet material, lecture slides and so on? Reviewing can also mean , you type notes on your computer / mac. Personally I prefered to use a mindmap (Novamind) for each class session.

Supplementary reading: First you should become familiar with reading and note taking techniques (My favorite SQR3). Then, once your read the assigned material compare your lecture notes to the reviewed notes. Does it all match to your notes / mindmap. If not, add it.

Homework: Now do the assignments. If you don't understand something, write it down. Take it into your discussion group.

Discussing: If you have a study group or partner now meet him and discuss your notes and homework problems.

Exam Prep: Take all the material you have gathered and make it ready for your exam preps: Use the notes to make flashcards of all conentent worthy to be remembered, make a list of textbook and professor questions you defnitly want to review at the end. ( Mostly you will encounter such question in the lectures of your professor. )

Filing: This is likly the most controversial issue and depends wether you have taken a lecture for credits or because of what you learned there can help you in the future. In this case, you should file your notes well in some way or the other.

The ultimate filing is the personal reference collection many scholars prefer to have, but filing can be a lot of work. Any kind of Wiki / Vodoo / Journaler ( DevonThink suggestion comes into this category. I currently stumble arround with slipbox http://markusguhe.net/slipbox/ which offers a integration of bibtex. If you don't mind the work of organizing a sound system of notes go for it.

Personally I think for normal studies a context system is more than enough. Your brain can remember in what course it studied what issue. So, for the sake of gtd, a course is a project. Hence, file your notes where you file all your projects, either virtually on your mac or physically. Additionally, you may want to write a list of keywords for each project referencing to your notes / files / mindmaps.

Well, this is I think enough encouragement for better note taking embedded into a study system. At the end of your studies you will have found your system, the latest.

Here are some last points to get you startet that may help you to develop your system:

1. How important is portability - do you work at home in a dedicated studying environment or in the library?
2. Do you need physical interaction (like paper has it) with your notes?
3. How do your notes of lectures and reading add up to studies?
4. How will your notetaking environment help you to prepare for exams, assignments, essays, presentations?
5. Can or do you want to use the notes in 5 years or 10 years?
6. How do you think? Are your more of a latheral type or a filing drawer type - does your note system fit your thinking ?
7. Do you study for the sake of a degree or to become a member of the scientific community?
8. How much time do you like to dedicate?
9. Can you apply Keep it Simple Principle ? - A wiki can be hell of work if you need to back up the database, update it etc.
10. Can other kind of notes or reference material be linked into your system. (Do you want to have literature refernce, author reference ? )
11. Do you need to embed media into your notes . Drawings, Formulas, (Movies, Sounds)
12. Will the work with your system interrupt flow principle?
13. Does fire, theft, physical damage, water destroy your system?
14. Do you want / need to share your system with others?