I don't keep an inventory per say, but I have a very good memory, and my traincase is very organized. I notice immediately if something is missing.
I did have one incident during prom season... I like to go back home and make some money by doing m/u for girls going to prom. Last year, I did a girl who I knew really well, just a year below me. She asked me if she could bring the lipgloss that I used on her (MAC Flashmode) to the dance w/ her so she could reapply for pictures. I said sure. A week later, I called her asking for it and she informed me that she "lost" it. Promised she'd buy me a replacement. It's been a year and I've received no replacement! And what irks me the most is I think she just wanted to keep it for herself, she didn't really lose it.
Anyways, since I'm in college, I keep my traincase locked and I don't let *anyone* share my m/u, unless I'm putting it on them and then putting it back into my case lol. Honestly, all my friends think I'm crazy anyways, so I really don't have too much of a problem w/ it.
I only let my cousin touch my stash, and it's because she's a MAC addict too. We split pigments n'stuff and anytime she wants a sample, I'm happy to oblige.