I cut 5", 2.5" squares and 2.5 " strips mostly. I used to cut 10" squares, 6.5" squares, 4" squares and 3" squares but found after time that use the 5 and 2.5 options WAY more often than any of the others. This is based only on what I found I use the most. No particular rhyme or reason. I also keep the scraps from my bias binding. I use them as binding on scrappy quilts.
When I have scraps smaller than 2.5" or long trimmings that are say less than 2.5, I drop them in a grocery bag and when the bag sets full I use them as stuffing for donation dog bed for the local shelter. So I am "throwing out" small scraps but they are being used rather than being turned into trash in a landfill.