You can microwave the soil like you said, and I think the sheer number of fungus gnats will decrease as you kill their little eggies (which I presume they lay in the fancy soil). If you wanted to nuke them, dampen the soil and microwave for 5 minutes. If you take it out and it's all steamy, you're good; if it's not steamy yet, microwave longer. Steam indicates the water in the soil has boiled, essentially killing most things in the soil (like your little gnats). After you microwave your soil and the existing gnats come back, they're going to try to go and lay there again. Try to nuke the soil every 3-5 days during the normal lifespan of the fungus gnats (2-4 weeks? You should look that up . . . ) and see if you can't kill off the population that way

If you wanted to go for a different lay medium, I know a lot of people mix sphagnum moss with vermiculite or soil, some people use only sphagnum. There are a lot of different options.  I know some people do use perlite, hatchrite, or just vermiculite in their lay boxes, but more people use those media simply for incubating the eggies.  You might want to try a mixture of coir and sphagnum moss if heating the soil doesn't do the trick for you; just be sure if you do use the coir that you take the eggs out of there before they stain (I don't believe I have read anything about the staining being bad for the hatchlings, but most suggest to just take the eggs out ASAP)

what about putting a few carniverous plants on the shelves around the cages? 

Hmmmmm .... never thought of that. Which plants do you suggest?

there are all sorts of cool carniverous plants. keeping them often seems to go hand-in-hand with dart frogs too; it's gotta be all the damn fruit flies :)

there are so many different types of pitcher plants that are just really cool, and also varieties of honeydews and others. if you have any frog shows in your area (or exotic pet shops catering to frog people) you should be able to get a good variety locally. if not, you can find a place online that will sell them.

if the plants get plenty of bugs, they don't need much at all in the way of light. so if the bug population goes down and the plants are looking a little pukey, just give them a bit of UV and they'll perk right up; and as they're tropical, mostly, they don't like to get too dry.

Fungus Gnats!!!

They won't stay out of my herb garden!!!

Here is the scoop.
The hardest part is breaking the life cycle and preventing NEW gnats from finding their way in. The gnats feed off of mycorrhizae mycelium and they must smell some of it in your substrate... Mycorrihizae is a benefical fungus that lives in the soil ecosystem and helps the soil food web. Gnats LOVE it. They smell it, fly in, dive bomb your substrate, and then the next thing you know you have millions of gnat larva infesting the top layers of the substrate.

They pupate, and transform into new tiny tiny dust sized gnats which grow up to start the BS all over again. Sometimes if you substrate dries out the pupa can be seen roving out of the soil climbing up and swarming (looks like light brown dust) looking for moisture.

(Reason I'm Explaining all this is that knowing how they operate is Key to their removal)  

First step is to go to your local indoor garden store and pick up some YELLOW sticky pest cards. Place these around your substrate and in the general "Gnat" area. Next you are going to have to treat the substrate, and then make it UNDESIRABLE to the adults. I'm not quite certain how to go about this without poisoning your eggs, but I will give you the rundown on what us gardeners do to keep them from killing our plants. Right now I'm experimenting with a spray solution that is a natural pest preventative and removal, the recipe is 5ml peppermint castile soap, 5ml 91% Iso alcohol (found at meijer), and 1L water. I put this solution in a spray bottle and saturate the plants and the top layer of the substrate (where they lay). If you believe your top layer is heavily infested with larva I would suggest removing the first 3 inches and then spraying.

Fungus Gnats won't lay in DRY substrate. They need the moisture to sustain their larva. Top dressing with coco is a good preventative method if you can keep it dry. I actually soak the coco in the solution to hyrdate it, and then top dress. Pearlite works great too but it's more expensive, they won't lay in pearlite because it won't sustain the larva and it won't harbor Myco fungus as well. But since you are using your substrate for hatching not gardening, you might want to just go with the pearlite!!! 

If you have a terrarium and live potted plants they have most likely infested the root systems, chewed all the root hairs off the plants, (where the myco works) and the plant is facing death if not already on it's way out. You will have to soil drench with insecticide to kill all the larva, and then start rebuilding the root systems. If you have delicates in there and can't use the peppermint soap mix I would suggest getting new plants and substrate and starting fresh. They lay millions of eggs and they are constantly re-cycling making more gnats. Best bet is to start with fresh substrate if you can!

Good Luck!

Thanks so much for all the info!

The problem I'm having is that my female cresteds lay in the substrate. I have a plastic shoebox full of this damp peat moss, a lid on top with two holes cut in it, and it stays very humid. It has to be damp for the females to lay in it - they won't lay in dry substrate.

I dump the old substrate and put fresh in often to try to keep the gnats under control but in the last couple of weeks, it just doesn't seem to be helping. My guess is, they are in the substrate straight out of the bag and when I get it damp and put the lid on, they thrive.

Soooo .... I guess I'm going to try the microwave thing. I'm hoping if I microwave every couple of days, it will kill off whatever larva is in the substrate. I'm going to try to find some of the yellow sticky cards too. Will these work if put up on top of my cages? The cards would be approximately 3 ft above where the substrate is but I can't really have the sticky cards in where my geckos are.

I'm just not sure about using the peppermint/soap mix .... not sure what reaction my geckos could have from it. These geckos don't drink out of a water bowl. I mist their tanks and they lick it off of, well, everything ;) .... so I have to careful about what's in their tanks because they will end up licking it eventually.

I guess I'm going to go microwave some dirt!! I hope this works ......

I forgot to mention the females don't just stand on top of this substrate and lay their eggs, they dig with their noses and sometimes completely submerge their bodies in order to lay their eggs in a hole in the substrate. They then use their arms and noses to fill the hole back in and smooth out the top. The whole process takes hours (sometimes a whole day) so they are in this substrate. That's why I'm so hesitant about what I use to treat these gnats.

if microwaving doesn't work um i suggest trying a different medium for your laybox.

They very well could be coming in the moss. It is VERY common for gnats to be found in organic soils ect... If this is the case then get a cheap metal sheet pan from Walmart and bake your moss AS SOON as it comes in your front door. The yellow cards can be put anywhere in the area, they will smell the glue and see the color and it attracts them. BE CAREFUL. That stuff is SUPER sticky and i've literally got it in my hair before and all over my house and it's bad. Goo Gone will remove it. 

Yeah if they are lickers you don't want anything but pure water in that enviroment. 

I think you'll be good with the baking and cards :)

I sure hope so! Thanks so much for all your help =) ..... I'll update this thread in a few days with whether or not it works.

A jar or cup of apple cider vinegar works well I use it and it works good.The sweet taste attracts them and they drown in it.Good thing is its non toxic.