What are some low fat butter substitutes for cookies?

You are asking not just to substitute for butter, but to reduce the total amount of fat in cookies.
All of the most common butter substitutes are going to be oils, margarine or other fats since they will perform similarly in the chemistry of the cookie. This makes it difficult to offer a simple substitution.

Instead, I recommend taking the approach of making cookies that are naturally lower in fat such as:

• Meringues - zero fat
• Macaroons - little fat, just in the coconut
• Macrons (french style) - little fat, without the filling -- just from the nut powder

or using recipes designed specifically to have lower fat content. If you google "reduced fat cookie recipe" you will find a wealth of results.

One site that looks promising, although I cannot vouch for it as I haven't tried the recipes is:

Good housekeeping's reduced fat cookie recipes

Another source for lower calorie recipes that are often pretty good, although not targeted specifically at reducing fat is:

Cooking light

Since fat contributes a lot of calories, you may have luck with their recipes.

The benefit of using recipes designed for less fat is that they are (from reputable sources) tested and likely to give you a better outcome than simply trying to substitute in a traditional recipe.

Also, you can try simply reducing the amount of fat in the cookie. This is going to be tricky as it will modify the chemistry, but you may be able to get away with a 1/4 to 1/3 reduction before you get completely unpalatable results, but this will require testing on a recipe by recipe basis. It also will not work well for cookies based on the creaming method, as the fat medium is part of the leavening (the purpose of the creaming method is to create a solid fat/air foam).

One final thought: some people say you can substitute apple sauce. You might try this on a recipe by recipe basis, but it will completely change the cookie. I think you will get better results with recipes created from the ground up to use less fat.