So apparently during the torrential downpours we got last week, my Miata got somewhat flooded inside. Hadn't driven it all week and went to drive it last night and there was about 2 inches of water in the passenger side footwell and it stinks pretty bad. I've soaked up the water and will be leaving it in the sun to air dry, but does anyone have any tips to getting the stink out? Any particular carpet cleaners that will do the trick, preferably that will also work on the passenger seat (cloth)? I think it got wet too and has just already dried, but I think it's still contributing to the stench.

I had the same thing happen to a car I owned. I shop vac'd as much of the water out that I could, left all the doors/windows open and parked in the full sun for a day first.
After it dried, I picked up some Ozium spray at AutoZone. Sprayed it throughout the car and ON the carpet itself. Closed up the car and left it for a day.
When I opened it up it was good as new and the mildew/odor was gone and never came back.
[ame="http://www.amazon.com/Glycol-Ized-Professional-Sanitizer-Freshener-Original/dp/B000FEPW40"]Amazon.com: Ozium Glycol-Ized Professional Air Sanitizer / Freshener Original Scent, 0.8 oz. aerosol (OZ-1): Automotive[/ame]

Awesome, thanks. I'm going to wait until Thursday when it will be sunnier and warmer and leave it in my driveway with the top down all day Friday and Saturday. Then I'll get some of that spray.

This stuff works great: http://www.odoban.com/products/odobanr-ready-to-use/original-eucalyptus-scent.php

They sell it at Home Depot...

I'd also get a tub of Desiccant (most grocery stores have it, asking is the easiest way to find it)
Leave the tub open sitting on the floorboard for a few days and it'll soak up any leftover moisture...

Thanks, Alain. That stuff looks perfect. Lowe's has some so I will be getting some today and leave in the car for the next couple days.

http://www.lowes.com/pd_2538-994-FG60MT_0__?productId=3054901&Ntt=damp+rid&pl=1¤tURL=%2Fpl__0__s%3FNtt%3Ddamp%2Brid&facetInfo=