Personally, for my boots, I use Dettol. It's a highly concentrated, and incredibly effective, antiseptic/antibacterial that will kill anything microbial that even thinks of going near it. I pour a capful into each boot, add hot water, and walk away. In the morning I empty each boot, refill with fresh hot water a few times, sometimes let the last refill sit for a bit, and there you go. No additional perfumes added but its normal odor isn't (to my nose) all that unpleasant. And not a hint of musty-dive-feet afterwards. In fact it takes a while for the sweaty feet odor to return.
I read the recommendation for its use on a freediving message board - the spearfishers like it because although we humans can smell it, apparently fish cannot..... plus it masks the odor of Human Hunting Fish quite effectively (apparently).
Found at Canadian and British drug stores/pharmacies. For some odd reason it wasn't available in the States when the spearos were posting about it - although things may have changed.
Edit: forgot to add that I do indeed periodically soak my entire wetsuit in a Dettol solution as well - I fill a wash tub with hot awter, pile in teh neoprene, and add about 2 or 3 capfuls of Dettol. (lighter concentration than the boots use)