Another area where in recent years I've gained some respect for folk theories is economics. Now of course, folk economics is even more full of falsities and fallacies than folk physics, and a basic education in economics will rectify a lot of these. However, at the same time, "scientific" economics has its own share of awful fallacies that have become a firmly established part of its conventional wisdom, and are happily parroted by legions of economists eager to scoff at anyone who questions them as an ignoramus or crackpot. On some issues where I would myself scoff at folk theories a few years ago, I have come to realize that they may actually be closer to reality than the overconfident assertions of economists.
In particular, if your folk economics intuition tells you that you're getting shafted but learned economists nevertheless keep assuring you that it's all in your own best interest, there's a pretty good chance that your intuition is pointing in the right direction while their assurances are just clever ideological propaganda.
I'd be interested in a LW or Discussion post by you on this topic.
Here's an interesting but very old paper - two theories of Heat Control.
It discusses mental models of home heating systems (thermostats) non-experts use.
These models tend to be extremely wrong from theoretical perspective, but surprisingly useful in practice.
The findings are applicable to a much wider range of subjects than just thermostats, and have certain epistemological significance, especially with regard to compartmentalization.