I've found that some cleaning solutions work partially, but the best way to reduce the smell is to use some sort of insole. In my Sperry Top-siders I removed the sole and used Johnston & Murphy's Dryz Insoles. They are comfortable, although they feel a little odd at first on your bare feet, but combined with Amenity Foot & Shoe Spray, you can pretty much reduce the smell to barely noticeable.
This may sound rediculous but it works well. clean the outside with a quick wash (the same you would when cleaning a pair of white shoes) and then put them in the dishwasher....yea dishwasher (of course with nothing else inside - other than other shoes)and wash them like a load fo dishes and then put em out in the sun to dry.
In order to get rid of the stank smell. toss them in the washer machine with detergent. Then let them sun dry. The next time you wear boat shoes make sure to line the inside with gold bonds powder or just regular baby powder.
I know they're technically socks, but you can't see them at all. I use these for all my slip-on shoes. Mens No Show Footies - http://www.journeys.com/product.aspx?id=80073&g=guys&p=app&c=854&m=SM
Fish stink, so do feet. Use the Amenity Foot & Shoe Spray This product is a lifesaver for all those around you. Keeps feet and shoes fresh and gives it a nice smell.
It's good to see that some people have an idea of what to do. I would have said, "To get rid of the smell, get rid of the shoes." Sounds flippant, but here is something else to think about. What brand are they? My great-grandfather used to say, "Every now and then, you come across a real bargain. Most of the time, though, you get what you pay for." He's right, and this especially holds true for shoes. If you do end up having to toss them, go to L.L.Bean,at www.llbean.com, or Cabela's at www.cabelas.com and check out what they have to offer in the way of boat and deck shoes. Good companies, good products, good customer service and they stand by their merchandise.
Banana Republic also makes a great no-show loafer sock: http://bananarepublic.gap.com/browse/product.do?cid=10865&vid=1&pid=555740&scid=555740012
The odor is probably from sweat. Baby powder and/or drying sheets gets rid of the smell and the baby powder will help w/ sweat
I think most people find that regardless of how you take care of your boat shoes, if you go sock-less, they're bound to err or the smelly side. However, if you use a pinch of Gold Bond Foot Powder you can significantly prolong the life of your shoes. The powder can help reduce and absorb your sweat. Still you'll find that your kicks will eventually start to smell but not till much later.
Another option is insoles, you can pick or a pair of Dr. Scholl's and change them when your shoes begin to smell instead of buying a whole new pair outright.
I've found that some cleaning solutions work partially, but the best way to reduce the smell is to use some sort of insole. In my Sperry Top-siders I removed the sole and used Johnston & Murphy's Dryz Insoles. They are comfortable, although they feel a little odd at first on your bare feet, but combined with Amenity Foot & Shoe Spray, you can pretty much reduce the smell to barely noticeable.
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You're right to not wear socks with boat shoes if you're under 40. As for the smell... I haven't learned of anything short of getting a new pair which I tend to do every year or two of heavy wear. The good thing is that they're relatively inexpensive and break in quickly. If it's really hot out (ie a heavy foot sweat day) skip the boat shoes and go for sandals.