I like to use a variety of jams for taste and color on my cookie plate. My favorites are red raspberry, apricot, and quince.
If you want to avoid sugar completely, you can dot the cookies with an almond, or a sliver of dried fruit like dried apricot or a few raisins before baking. Or try a fruit butter such as apple or pear butter.
I have heard of using whole wheat pastry flour instead of the regular unbleached white flour but I have yet to try it. I imagine it would be pretty good, adding to the nutty taste and hearty texture.
The unbaked dough keeps very well in the refrigerator for about two days if kept well-covered.
These thumbprints are an ubiquitous vegan treat and I'm sure there are many variations out there worth exploring. Have you ever added coconut, or used pecans or hazelnuts? Tell us in the comments!