I guess I use a combination of things that everyone else has already mentioned.
I use a LARGE 3 ring binder for completed projects- with gauge swatch(not often!), yarn stands, yarn description, brief pattern description/reference, washing instructions, who it was for, dimensions of finished project and a photo. I just keep adding binders as one gets full.
Single page(s) patterns, small leaflets, etc are kept in an accordion file folder tabbed by type: Scarves/hats, afghans, dog sweaters, etc. Books/Ancient Magazines are kept on their shelf.
I use a lot of Stitch 'Dictionaries' for a basic pattern, and fake it from there. I like to make a copy of the page in the book/leaflet/magazine, carry it with the WIP, then file it w/the completed project info in the 3-ring binder.
For online patterns that I find - to make "one day": I print them to a PDF file using a free version of PDF Factory ( http://www.fineprint.com/products/pdffactory/index.html ) then save them in folders by type on my hard drive. I like this method (1) because I don't use paper til I actually use the pattern; (2) I have the pattern even if the site where it was disappears.
I used to use a program called KeyNote for keeping track of everything, but since the switch to Vista x64, I've had to change to a program called MyNotesKeeper (I think it costs about $30, after a 30-day free trial). It's a tabbed notes keeper that lets me keep every trivial bit of info in my life organized in one file. I have one tab for Personal, under it is, among other things, my misc crochet notes. I suppose if I was as prolific as some of ya'll, I'd have a separate Noteskeeper file just for crochet projects, tabbed by type. Anyway, I like the program, and you can insert pictures too.
I would recommend PDF Factory: because it's free, and printing or trying to save website pages sucks! PDF Factory sits with your printers, so you just choose 'Print' from any software/website and select PDF Factory instead of your regular printer. Instead of printing, it opens as a PDF file that you can save to where ever you want. You can't edit anything though. It's useful!
Best Regards to All,