I keep the ones that I know will go into a quilt together. I keep the pattern and rotary cutting instructions with that batch, ready to go.
After specific projects, I sort by type or novelty: wide backings, Civil War repros, 30's repro's, solids and tone-on-tone for applique, baby, juvenile, Christmas, Autumn, gardening, sewing, Texas, etc.
Within those groups, I sort by color.