Know who uses your resources. If you have a small group of users, you can set up accounts each quarter for all of them on a local file server and force your machines to log in to that server before they can use your resources. You can check identification at the door, or do spot checks during the day. Whatever you do, it is best to ensure that those rules are posted clearly, so that the people who use your facility will know what to expect. Secure your physical machines.
Theft is always a problem.
CPUs, memory, and even the mouse at a workstation are prime targets. Lockdown kits are not cheap, but they do save on replacement costs in the long run. Marking your equipment with large engraved identifiers also makes stealing it less attractive. Have your staff keep an eye on things. Your security guard or support staff should know that it is part of their job to watch for theft, abuse, and illegal activities.