Any time in Mother Nature's bosom (aka outdoors) is going to be best for all your plants. Lots of full sunlight and fresh air. The fresh air and air circulation is good versus fungus gnats who love the overly moist soil and still air found indoors.

The thymes and rosemary should be in very well draining soil - soil somewhat like bonsai soil. The others prefer soil that is average to well-draining. And none of these plants should be sitting in water or overly moist soil. I personally would err on the side of too little rather than too much water with any of these plants kept indoors.

Be sure to also check out the container gardening forum for lots of general container advice.

FataMorgana

I do keep a close eye on how much I'm watering, so I do know that isn't the problem. The thyme and rosemary have gravel in the bottoms to help keep them better aerated (plus the pots do have overflow drains). I hadn't heard of bonsai type soil for those, but it makes sense, especially for the tree (rosemary). I did check the container forum, and most of it doesn't really seem to apply to the arid types of herbs.

I also realize now that I didn't spell mulch right for the title. Oops. I was wondering mostly if I should consider mulching them to contain more moisture--Denver is dry! I've tried the pea gravel, and was considering sand too.

Fata,

Thank you for the tip about the bonsai soil. Though spendy, I did get a small bag and mix it with the potting soil to repot. In the last week and a half, I am starting to see new growth and flowers, with no more blackening from root rot, so it appears they are happy with the new situation.

Though, if anyone has ideas on a good mulch for indoor potted arid herbs, I would still love to hear!

Using mulch inside will make it even harder to get rid of the fungus gnat and not correct the problems you're having. My general impression is that your watering system is the problem. How does your self watering system work?

I have come to the conclusion that I may have to invest in some nematodes to combat the gnats, since the sticky traps are barely keeping it under control, and with herbs that we regularly use for cooking, I don't use soap or neem very often. I think they came with the old rotten potting soil that I replaced. The new mix of soil for the arid herbs, and simply new soil for the non arid herbs seems to be taking care of my plants properly.

As to the watering question--I am very aware of the watering requirements for my herbs. I think the problem that I was having was all with the soil--completely bone dry on top, yet stinky wet in the bottom. I was watering them only when the top inch or two was dry, but when I repotted, I discovered that the top 3-4" was bone dry, yet keeping all the water in the bottom and creating my root rot issues rather than feeding the plants. The pots that I have are of the following type:
http://www.noveltymfg.com/Products/RoundPlanters/NapaPlanters/ArtstonePlanters-WaterMinder/tabid/144/Default.aspx
I chose these because I liked how they look, and the variety of sizes. They are also not heavy to move around (at least as light as a 12" pot full of soil can be) as a ceramic pot, yet look nicer than plastic. They basically have a small plastic disc in the bottom, leaving room for a water reservoir that I try not to fill for the arid herbs, giving them some extra airflow. I have the plugs removed so as not to keep water in the bottom, and do not overwater them. I also place a variety of sizes of lava rocks in the bottom to ensure proper drainage for the arid herbs.

As stated, the new soil seems to be working well for me--holding the moisture throughout, and it takes much longer for the top layer to dry out now. A mulch may no longer be needed. When it warms up, then I can move them all out for a while, add some nematodes to kill gnat larvae, and then bring them in a couple at a time to ensure that the pests are gone before grouping them all back under the lights. I just don't have room outside to keep them out all summer (and my 2&4 yr old bother them when out, but not inside for some reason).