I have used Diatomaceous Earth and Gnat Nix Fungus Control Top Dressing. The DE is a mess to work with. I would go with the Gnat Nix that you can get on line or at places like your local hydroponics shop or even home depot. Put an inch or two on top of your grow medium and it is supposed to kill the larva as they crawl out of the dirt and turn into flys. Also, get some yellow sticky stakes from amazon.com; they are like fly paper for gnats. You want to catch the flying gnats too before they lay more eggs in your soil. The gnats have a 30 day life cycle so it may take some time to kill them all. Try to keep count on your sticky stakes so you can see if the fly population is going down.
You can also use an organic product from GreenwayNutrients.com called "No Fungus Gnats" to kill the larva in the soil. Just mix about 1.6 oz per gallon (half the spray strength on the bottle) and apply it during your mid week watering cycle and then every 5 days or so. I use all three of them myself.
But the DE is just a powdery mess and gets over everything like leaves, stems, etc. The DE mess gets my attention because it looks a bit like mold.
