My two choices were proper subwoofer placement and choosing the right subwoofer cable. The first response is probably self-explanatory as placement is key...I don't know who would argue that point.
However, cable choice wasn't chosen a lot. I chose it because I had an issue with my subwoofer cable. When I moved into my new house, I connected my sub using in-wall cable that I ran while the house was under construction. The sub would perform fine when everything was on and it was getting a signal. When I would turn off the receiver, however, I would get this hum that immediately went away when I turned the receiver back on. I switched from the in-wall cabling to a sub cable that I had lying around and the hum would still appear. Only after switching to a high-quality, well-insulated cable did the him disappear. This might go overlooked by some but using a cheap cable can have bad consequences.