I've been using Xournal for notes, problem sets, etc. for the last 5 years. It doesn't do handwriting recognition, etc., but I find that this is a good thing -

I've been using Xournal for notes, problem sets, etc. for the last 5 years. It doesn't do handwriting recognition, etc., but I find that this is a good thing -- that way I don't ever have to go back and fix recognition errors, and unless you are preparing something for publication, typesetting math is a waste of time.