The ones that are really geologic specimens are labeled with tiny laminated labels stuck to the bottom with mineral tack--those are basically crystals on some sort of matrix, and they have the name & mining location on them. I'm now doing this whether I bought the specimen for use in a grid or just for display. When a crystal of this sort comes into the house, I just type up the label in a 6pt font & print it out.
Crystals that are meant for crystal grids are currently in ziplocs that I need to label, and those bags are in a leather wrapped hatbox. Miscellaneous tumblestones that I only have one or two of that are not actively "working" in a grid or display are piled in a bowl on my desk, and that bowl is surrounded by a bunch of other crystals, like clear quartz and amethyst clusters.
I should probably stick a label with stone names to the bottom of each grid or dish display I have, now that I think about it.