At the moment I'm in favor of discarding anything shorter than 2", with the exception of a couple of bins of 2x and 1x cutoffs that live by the chop-saw. We've got two big shelving units that are essentially 4' x 8' plywood shelves in a steel frame, 4 shelves each.
IMO they suck, too deep to be useful, might
build something like cubbies within each shelf.
In general I tried to keep dimensional wood together, 2x, 1x, and 'other' for lumber,
grouped by size (<3', <4', <6', <8' or whatever makes sense for what you've got). With our 4' deep shelves, i'm limited on what I can slide straight in.
One thing we definitely try to do is keep new lumber separate from used. Use the used wood if you can, and always grab the shortest piece that will work is the general rule.