I have been using index cards when studying math, at least now.
It's really useful to write down definitions and theorems on one side (one definition/theorem per card) and explanations of why it's useful on the other side (possibly sketching the proof).
It's been really useful while reading through Kirillov's Lectures on tensor categories and modular functor (eprint [math.sunysb.edu]).
Gel'fand's Generalized Functions reads like a dinner table conversation between mathematicians, without formal definitions in the grocery-list Bourbakist manner. Index cards help out a lot here, enabling you to write down where references are (which was, coincidentally, why they were invented in the first place!).
It's also wonderful when you begin to write a book, you can just collate the index cards of theorems and definitions. Then writing is just a matter of inserting literary "glue" between already existing material.
One can form a wiki [http://takingnotenow.blogspot.com] using index cards.
But instead I prefer to organize notes [studygs.net] slightly differently. It also enables me to "automatically" cite by keeping track of the source in the upper right corner, and label it as a definition or a theorem in the upper left corner.
Plus I am not married to any collation in this scheme. On the other hand, I have to look through all my notes to get to various definitions --- there is no organization to it!
Just more stuff to ponder...