The smaller scraps I cut into 2 1/2" squares as I have a few patterns for scrappy quilts I'd like to try. I don't keep anything smaller than 2 1/2" square. The slightly larger scraps I either leave as is or I cut into 2 1/2" strips. The larger (less than a fat quarter sort of) get kept in a bin that is separate from my fat quarters. I find lots of patterns that call for a fat quarter often don't use the whole piece so I can often use these sorts of scraps to cut those pieces needed...
It's not a perfect system, and there are times I think of changing my "system" but nothing I've seen or read about seems better, so here I sit....