I take class notes on my Powerbook, and often I take mathematical notes that involve superscripts and subscripts. To make it more convenient for me to take clean notes, as opposed to notes filled with “x^2″ and “y_j”, I looked into changing the key bindings in OS X. You need to create a file at ~/Library/KeyBindings/DefaultKeyBinding.dict, and if the directory KeyBindings doesn’t exist, you should create it (mkdir ~/Library/KeyBindings). In this file, you can specify different key combinations and the resulting action that should occur. Here’s my DefaultKeyBinding.dict:
I used this tutorial, which has lots of good examples, to create mine.
What you need is a program called Mathcad. I always used it in my physical chemistry classes for taking mathy notes. It solves equations and all sorts of stuff, too. Unfortunately, I think it only works in Windows.