What are your favorite ways to use whole wheat pastry flour? And how do you usually substitute it for other types of flour?

I liberally substitute all of the all purpose flour for whole wheat pastry flour--it's really up to you what ratio. To add to K'lee's answer, you should use it for recipes that rely on baking soda or baking powder, not in recipes that rely on yeast. E.g. biscuits, pie crust, quick breads, cookies.

Heidi Swanson has several recipes that use whole wheat pastry flour (see http://www.101cookbooks.com/ingredient/whole%20wheat%20pastry%20flour).

In particular, I love her recipe for Marathon Cookies: http://www.101cookbooks.com/archives/marathon-cookies-recipe.html

Since pastry flour has a very low protein content, it's best used in recipes that don't rely on a lot of gluten and a lighter, crumblier texture is desired.