I store mine by size - 1.5, 2, 2.5 - when I am ready to go, I put out ten coffee filters and sort one of each in each of the coffee filters. If I have five of one, then it goes only onto five filters, if I have nine then only nine go out, when I am done each coffee filter has a large supply of one of each that I then start working into squares/blocks. I did this for 290 nine patches made from 2 inch squares. The same fabrics are used all over the quilt but each block is different. I like this method better than just grabbing since I tended to grab the same fabrics over and over and it looked too planned. I am one of those people who sew two lines when doing half square triangles so the part that is cut off is trimmed down to one of the above sizes and they can be tossed in every once in a while - it uses all those little pieces that get trimmed down. I love a book called "Adventures with Leaders and Enders" by Bonnie K. Hunter - I have made three quilts from this book and the fourth one is just waiting for the perfect outer border.
I am pretty sure there is no right or wrong way - just your way and what works for you.
I just got an envelope full of scraps from luvTooQuilt (I sent her postage and she sent fabric scraps she didn't want anymore) - yahoo! I can hardly wait to press them all and trim them to their biggest sizes - they will add a little something to my quilts because they will be different than everything else I have.