Stick those containers of Damp Rid around the basement. BJs sells multi packs
Try pouring scoopable kitty litter on it and let it sit for a while to soak up the smell. Then sweep/vacuum. After that, pour a little baking soda or Carpet Fresh on it for a great smell.
Bleach /water sprayed everywhere is what a recovery business did in my flooded basement after drying it out well with large fans. I've used charcoal briquettes scattered around to absorb musty odors before as well. Perhaps both will help you get rid of your problem.
There is a product called Benefect - safer and less odor than bleach that will kill the mold spores. Made from the thyme plant/herb and smells like thyme. I purchase from a restoration (mold, water, fire) store. It's also great for cleaning your bath room. Here's the link to their web site: http://www.benefect.com/CA/products/disinfectant.php
use baking soda to absorb the smell. Be generous and leave for a couple of days. Then use vacuum to pick up.
Rent an ozone machine for a day and let it run for a few hours. Air will smell like fresh air after a cleansing rain.
Bring in Dehumidifiers to draw the damp out! If you are Insured - check out your Policy!