I would highly recommend checking out "The Definitive Guide to Cleaning Vibram Five Fingers" on birthdayshoes.com 

Link: http://birthdayshoes.com/the-definitive-guide-to-cleaning-vibram-five-fingers-a-k-a-how-to-get-the-smell-out-of-your-vibrams

I can personally attest to the success of daily wiping of the feet with tea tree oil, and soaking the shoes in a basin with a few antibacterial denture tablets (2 in each shoe for a small basin, more for something larger). For really nasty stank, an overnight soak may be warranted. Rinse well, then make sure that the shoes dry completely before wearing them again. Stuffing them with paper towel to wick moisture and then putting them in front of the vents at the bottom of the refrigerator works well to dry in less than a day. I don't know if regular denture tablets work the same, but generic antibacterial tablets seem to do the trick. Plus they leave your shoes smelling minty fresh. I'm sure they'd also taste minty if you were so keen to try.

My experience comes mostly from washing Merrell Barefoots, but I've tried denture tablets on VFFs and it seems to work equally well. By rotating between 2 pairs of shoes and following a tea tree oil regimen, the shoes tend to stay within an acceptable odor spectrum for 3 to 4 weeks before needing to be soaked again.