As a basic "rule", I organize my patterned papers by manufacturer. I like to keep collections together and I put the newest release at the front of the pile. In order to keep everything neat and tidy, I use Generations 12x12 plastic envelopes for all papers, including cardstock (which is separated by color family). I store non-themed collections in a pretty, handled market basket (as seen above) and the themed collections and cardstock in a 12x12 mesh milk crate. I also store any flat embellishments or sticker sheets with each collection.
I have one envelope filled with odds and ends like pieces of diecut papers to either use or trace and oddball pieces that no longer belong to a collection because I used it up (see below):
Earlier I mentioned my "basic" rule of organizing, but rules are meant to be broken, so I store themed collections separately, along with any themed embellishments. Here's my folder for fall/Halloween/Thanksgiving:
And here's an envelope of patriotic/Fourth of July:
I hope I gave you some ideas to get you started and I'm always open to new ideas so please share with me how your craft room is organized. :)