A little Pine Sol or similar disinfectant/sanitizer in the wash water (less than 1/4 cup to 4 gallons), perhaps in addition to a little mild laundry soap. If you wish, add a little fabric softener as well. Wash thoroughly (if it's really stinky, soak for a while) then rinse & hang to dry.

For booties, it helps if they can get REALLY dry, which means some sort of hangar or rack to hold them open & open-side down to drain. Some folk have devised contraptions with PVC tubing to direct hot air from a hair dryer into the boots. I know one person even devised a means to use the output from his car's heater to dry his booties while driving home! (use caution/common sense applying heat to neoprene - it's possible to get it TOO hot & melt it!)

Polypropylene or nylon clothing gets tossed in the regular laundry.

Enzymatic deodorizers like Sink the Stink are probably more environmentally friendly than Pine Sol, especially for use during a trip.

I haven't tried natural antibacterial agents like Tea Tree Oil, but that might also work and be fairly innocuous to the environment. I may try that when I wash gear after this weekend.

Val