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TiddlyWiki. It’s a bit different from the applications listed in the links you posted, but may be better for your purposes.
ADVANTAGES:
* Runs in your browser. Everything, including editing, happens in Javascript within one 500KB index.html file.
* Does math. Really. With jsMath plugged in, TiddlyWiki does LaTeX inline with 99.8% accuracy. It’s not technically perfect, but this particular theoretical physicist finds it to work quite satisfactorily. This is the single killer feature that no competing application can do AFAIK.
* You can rsync it to a webserver with trivial ease — if you want to. Check out for a seriously extensive example. The entire site is a TiddlyWiki. (And note that these were usually written the night before class).
* Hypertext, linking, and wiki-structure IF YOU WANT IT. Or you can just make it a bloody huge linear notebook. Or you can start writing and chunk it into hypertext later (when you have time).
* FOSS.

DISADVANTAGES:
* It’s not as easy to paste in random content as it might be with a dedicated application. There are things you can do with a binary executable that you can’t do with JavaScript running in a browser (like access the filesystem with abandon). To put it another way, it’s neither WYSIWYG nor Drag-n-Drop. More like a hypertext notebook in LaTeX.
* Not commercial, so there’s no professional support. On the other hand, it’s FOSS, so you can write your own plugins.

If you decide you like it, I’ll be happy to ship you my customized “bare” installation (basically, my own notebook with all the plugins, but with all my content taken out).

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Hmm. My hyperlink (supposed to be after “Check out…”) disappeared. I’ll try again in a couple of different ways. I referenced http://am473.ca which could also be inserted as an HREF to this online textbook.

If neither of those worked, I give up.

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I found out last time I was in school that I really enjoy taking long-hand notes IN class, then transcribing them to a typed format AFTER class.  As a first step to committing things to memory it works really well.  So the big question is: into what format should I be entering my notes?

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First I thought big.  What about a Wiki of my very own? It would do everything I needed and then some.   However, after playing with it for an hour I quickly realized it is a LOT more work than simple note-taking should be.  If my goal is to have a beautiful, well cross-referenced set of notes, Wiki might be the way to go.  But thats silly, I just want to be able to look up stuff while studying and not miss a homework deadline.  Nobody keeps notes nice enough to turn in.  Those are called Lecture Notes. Ha ha.

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So Im looking for some software to invest in to do my note-taking, homework-tracking, paper-researching, and any other labor-intensive schoolwork which could benefit from the organizational power of a computer.  Im not looking for a lot of bells and whistles, but built-in hypertext would be a pretty handy feature.

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I use a Macbook, and found some reviews of competing programs.  Lifehacker has a further list.  Have any of you Mac users out there tried out these tools?  Im open to suggestions and feedback, so geek out on me, here!  In fact, if I choose a tool based on your suggestion you will win a free thing.  Yes, a FREE THING! Ill even ship it to you.