I have a pretty large stash...the majority of mine is stored in crates turned on end and is by color, crates stacked 4 high, with a curtain in front to keep out sunlight...the crates are within a closet. Light colors/backgrounds are on the shelf above, with a piece of muslin draped over again to keep out sunlight.
Then I have another cupboard full of larger pieces of fabrics for borders and backings. And one dresser upstairs full of plaids, another full of batiks, florals and more plaids. Plus another tub of more plaids that don't fit (yet) into the other storage areas. I hope to keep using my plaids enough that all will fit into drawers soon.
Even room light can fade fabrics, not just sunlight, so try to keep your fabrics covered some way so they don't fade!