What's this crazytalk about organized patterns? Blasphemy!
Here is my system. I have a binder for patterns, they are in sheet protectors. Whenever I get a new magazine, I go through and put a post-it flag on anything I really like. I keep the magazine in magazine boxes that I can literally reach without getting out of my knitting chair. Yes, I am THAT lazy.
If I REALLY like a pattern and see myself making it, I scan it and save it to my computer in a file called knitting patterns. If I plan to make it eminently, I print it out and put it in the binder in a sheet protector. Usually I don't actually end up making it. I keep 3 projects on the needles at once, but I have more patterns in my "queue" than I could ever hope to knit.
This may not sound like much of a system, but it beats the heck out of my previous system which was to leave all of my dozens of knitting magazines splayed out on the floor around my knitting chair. Every Wednesday the cleaning lady would come and stack them in a neat pile and by the time she came back the following week I would have them helter skelter again. Most of my yarn stash would also be intermixed under, between and on top of the magazines.
Then once she brought her mother to "help", but I decided it was really to prove to her mom that someone as messy as me really does exist. I felt that it reflected badly on MY OWN mother (who is super type A/organized), so I made some changes. Put the magazines in proper magazine boxes and I keep the yarn in plastic bins. Mostly.