Caveat: I do not know if this will work for booties that have never been washed (does anybody actually admit to this?!).
It works wonderfully on my ancient Teva Protons and hasn’t harmed the neoprene or other material in any way.
1: Rinse booties in plain water to rid of sand, bugs, and other debris.
2: Fill bathroom sink or other container with hot water. Lather up with bar soap (the kind you bathe with). Put booties in the soup and let them soak in there. No need for long soaks; a couple of minutes is good.
Step 3: Drain sink and rinse booties with more plain water.
Step 4: Fill (or half-fill) sink again with warm or hot water. Add isopropyl alcohol. I did not measure proportion of alcohol to water, but it was less than 1:4, and I used 70% isopropyl; it comes in different strengths. Put booties in to soak for about a minute.
Step 5: Drain sink and rinse booties with plain water.
Step 6: Let dry, preferably outdoors in the sun.
Before adding the alcohol step, I sometimes got a lingering whiff of neoprene stink even after a good wash and sun-drying. The alcohol step got rid of that. MUCH nicer than using bleach.
How about…
a clothspin on your nose!
But seriously, many foul odors are caused by organic acids. Organic acids can be in their free (acid) form, or in their salt form. The free form is more volatile (and hence more stinky!). By soaking those booties in a solution of sodium bicarbonate (aka Arm and Hammer baking soda), you will put those nasty organic acids into their salt (non-stinky) form. Also, the salt form is more water soluble, so when you rinse the offending footwear, the salt-form organic acids will be rinsed away. As an added benefit, you’ll be using a safer chemical than isopropanol. Probably soak them overnight for best results, then rinse well.
Tony
Easy???
Sounds like a lot of work to me. 
Just throw them in the washing machine with some white vinegar. It really does work.
A cap full of…
bleach in a couple of gallons of water will do the same thing faster and easier.
Sink the Stink
Visit your local dive shop and get some Sink The Stink. Fill a sink, tub or other vessel with cool water and mix in a couple ounces of the stuff. Soak your stinky booties and then hang to dry. Stink sunk.
Rob
nope
bleach makes 'em worse. the buggers die on the surface but not deep inside. the live ones eat the dead ones and you have bugger dudu in your shoes.
:-p~
Sink the Stink. It's live enzymes that eat all the buggers and don't poop.
steve
Expensive overkill
Vinegar is much cheaper and if you put them through a wash cycle it will work just as well.
One word
Febreeze
http://www.procter.se/highres/jpg150/Febreeze/febreeze_150.JPG
In GA, booty is spelled different, and
has a different connotation. But soaking one’s booty is still helpful.
Febreeze hasn’t worked for me
It does not work on pet “mistakes,” either. For the latter, enzyme-based solutions work much better.
Febreeze is merely detergent mixed with extra perfume.