Perhaps you could make fake versions of common linux/unix tools, perhaps a wrapper to something like gcc that is usually just a pass through, but occasionally it would filter the output with Expect (or something) and occasionally introduce humourous error messages:

Internal compiler error: modulus segmentation beyond dangling pointer. Recompile with RTYPE_PRUNING=3?

Maybe it could get more cryptic or introduce more humorous errors over time. I like having something filter the shell too. Maybe make the 'z' key not work 10% of the time. It could take days before they understand the problem. They'll be swapping keyboards and all kinds of good stuff!

Just be sure you do a good job so they don't figure it out really quickly :)