My favorite pattern company is Burda. I subscribe to Burda World of Fashion and buy the envelope patterns as well. I came up with a method to organize the BWOF magazines that works very well for me.
I use only the plus-size designs in BWOF, so this method is manageable for me. I made a template using a word processing application. I import photographs and line drawings from the Burda website into the word processing document, print out the pages, then store them in a binder making a handy index.
I can flip through the index, select the pattern I want, then go to the issue and remove the desired pattern sheet. I store the issues and pattern sheets in a 13 pocket expanding file and the file is kept in my bookcase.
Works for me!