I just got a 2.1 speaker set and my subwoofer is on the floor near my feet, ~3 inches away from the rear end of my tower. Is this safe? (In case it is relevant, this is the set http://www.amazon.com/dp/B0027VT6V4/)
Yes, it is safe. Older HDDs didn't like being close to magnets, but your subwoofer is probably not big enough to affect the HDDs that are in the front-end of the case.