I should state right up front that I am probably not the person you want to come to for advice on keeping your knitting things organized. I have a lot of ideas on the subject, I grant you, but if you came into my office (please don't!) you would see that I have none of them in current practice.
Getting my knitting stuff in a better state is a perpetual resolution of mine, and I think I've got a plan -- or at least some good motivation -- that might carry me through at least the yarn organization part. I am a big fan of big bins and have several now on the high shelves lining my master bedroom closet holding things like all my cotton yarn or all my acrylics.
What I should have done before I put all that stuff up there is to log it all in my stash on Ravelry, along with the hundreds of knitting books I own, all my needles...yeah, that's probably never going to happen, but if you have a smaller stash than mine and want to keep better track of it all, Ravelry is a great organizational resource.
If you're looking for a non-digital way to keep track of all your knitting stuff (or just want to know what other options are out there) be sure to check out my article on organizing your knitting records, too. Even if you keep track of things on Ravelry you might also want to have a project notebook or scrapbook keeping track of knit gifts, for example.
If you've got any great tips for organizing the stuff of knitting, I'd sure love to hear them and I know I'm not the only one!