I like to collect everything in the closest chest to the entrance prior to hauling anything out, but, as was mentioned, don't just leave things on the ground except near base structures. Base structures will (AFIK) prevent them from spawning.

When mining ore, I also like to drop a chest to put the ore into just to make sure I don't leave it on the ground too long. If you care about the rocks, you can create stack of them, of course.