I haven't personally seen any tools go missing from our shop. Of course things will break (I have broken a tap before), but they get replaced, no big deal. We have a large rolling tool chest in which we store all non-power tools (except for the heat gun.) Everyone just knows that the tools have to get back in our room. We have labels on each drawer for what should be in it (I especially like the 7/16 drawer!) We color code the sizes of wrenches and nut drivers. The tool chest is right next to the door, so it is easy access since we take over the entire third floor of our school when we work. We store smaller parts like sensors, bearings, screws, rivets, etc. in two tiered part boxes. We have a student that really likes organizing and keeping things clean; it works out really well for us. My favorite equipment in the shop: a high quality screw driver set. Sure having a mill, lathe, 3D printer, etc. is nice, but you are missing out if you don't have nice screwdrivers. One last tip for organizing, we have two of
this type of table with
these accessories added (except for the drawers). We have one table with two desktop computers and a TV (the CAD table) and the other (the programming table) with one desktop, several laptops, and several programming things.