I had thought about organizing in some way, but I find my tastes change and some fabric just beg for a pattern that never interested me before. I've just decided to stop getting quilt magazines so I don't have sooooo many to look through every time I need a quilt idea. I do take a black marker and write on the front of a magazine the name of a pattern and page number of quilts I have done that I may need to find the pattern for when someone asks about it.
I spent hours going through and organizing patterns from a craft magazine that I got years ago using notebooks and page protectors, but I rarely use them now. It was really not worth all the work. So I've decided not to do that with quilting Mags. Just not let my collection grow too large.