I use regular cookie recipes but substitute whole wheat pastry flour for the white flour. Sometimes I use a combo of oat flour or a little almond flour & the WW pastry flour.

Yeah whole wheat pastry flour is an option.

Here is an interesting basic cookie recipe with variations:
http://www.fatfreevegan.com/desserts...as_dough.shtml

Someone recently submitted a gluten free vegan cookie recipe to the site. I can't vouch for it, haven't tried it, but it looks good.

http://www.3fatchicks.com/diet-recip...vegan-cookies/

Bob's Red Mill has a ton of different flours. When they started being available in local stores here, I started experimenting with different types. The Bob's Red Mill site has a ton of recipes for ideas. I've used white bean flour (very neutral taste), almond flour, WW pastry flour, etc. to make all kinds of things. It's getting easier nowadays to avoid white flour.

ETA: If you can't find these flours locally, they can be ordered online.