Start by removing the amp from the cabinet.
Try powering the woofer from a different amp, even a $5 thrift store receiver will do. Just make sure that there aren't any odd scraping noises. Also, meausre the DC resistance between the two wires going to the woofer (should be 4-8 Ohms).
If the woofer is OK, then pop the cover open on the amplifier and look for things that are out of place. In particular, look for caps that are bulgy or leaky, as well as for resistors that are burned or completely blown out!
There's also the slight chance that there are four wires leaving the subwoofer, and that they connect to at least three very distinct places on the board. If this is the case, some additional testing will need to be done.
-PB