You do have lots of options, and lots of bad ones at that.

Ultimately, note-taking is something that has more to do with your own personal style than anything else. Personally, taking notes on paper has always seemed highly inefficient - you can type faster than you can write and once you get a program down, it is much more efficient.

What I do, and what I'd suggest for anyone wanting to try something else... forget Tinderbox and DevonThink. They are nice products, but also expensive products. Also, the learning curve on both is rather high and in general, for most students, it will be overkill.

Yojimbo is great for a "file folder" but if you're syncng it between two computers, it can become very slow. And actually working in Yojimbo to take notes isn't terribly sufficient.

Your Mac probably came with OmniOutliner. Try that out, it's one of the fastest and best ways to take notes on a Mac, there is a bit of alearning curve, but not much of one. You can import links, pics, etc into the note. But what I like to do is the following.

I take my notes in OmniOutliner (you really don't need to pay for Pro) and also use a program called Curio by Zengobi (http://www.zengobi.com) it's basically a whiteboard for your Mac. Try it out, it's free to demo and reasonably priced if you buy it. You can put just about anything in there, tag it, add a due date, all sorts of things. You can also just drop in your notes from OmniOutliner or copy and paste them into a space. I tend to create one file for a semester and go from there.

It does put your files into a database file, but... most do. Long as you keep it backed up, it shouldn't be a problem.

I actually went into some detail on my blog Scholastici.us http://www.scholastici.us/2007/09/12/the-full-system-note-taking-scheduling-and-studying/ Regarding this exact subject. I hope this helps!