I have been buying up other people's scraps and unwanted fabrics and most of it comes in all mixed together. After washing I start sorting into piles and then box most of it. I then take boxes out and start ironning and then put it in a basket and take every week some time 10 minutes to hours to sort and put away. I sort both by theme (1930, civil war, floral), size scraps, FQ, and large pieces and color. I also toss and give away at the same time.
Bonnie Hunter
http://quiltville.com/scrapusersystem.shtml
has a wonderful system. I follow some ideas but am not as good at it as she is and I add my own touches for my own purposes.
I try to keep fabrics together where I am most likely to use them else I can't find them. So fo example I am big on kids I spy quilts and have a bin with cut squares and FQ with those types of fabrics. I also have an old plastic zippered bag froma comforter that is full with I Spy type kid's prints scraps.
All 1930 type fabric is in several plastic bins and are stored on a shelf together. I might even put patterns in it that I like.
I also have a shelf with UFO. Most are a pattern , fabric for that pattern and some are partially done. I might even store a ruler in it or other items needed but I am trying to avoid that because I "lost" some of my rulers that way. It is kind of like making my own kit.