I believe the 50ft unshielded CAT5E will 'work' fine, but over longer distances you allow the cable to be exposed to more interference and possibly degrade the quality of the signal. If you're only traveling 3-6 ft, i wouldn't think unshielded cable would make a difference, but that changes when you expose more and more of the cable to interference.
Also, keep in mind that at your work, unless you work in a high-end audio/video studio, they're not too concerned about the slight signal degradation when you're pulling an Excel spreadsheet over the network to your PC. However, that slight-to-moderate degradation might cause unwanted affects on your home theater system.
I look at it this way, if you're going to spend the money to build a decent home theater or to enjoy whole-home viewing, don't scimp on the wiring. You can always upgrade tv's, stereos, speakers, etc, but once you cover those wires with drywall, it's awfully hard to upgrade them.