I've converted all my favorite baked goods recipes. Here are some things I do:
Flour - I presoak non-sprouted flours (remember to account for soaking liquid), or use presprouted flours.
Oils - Any oils get replaced with coconut oil or butter.
Sweeteners - All sugars get replaced with sucanat/rapadura, honey, agave nectar, and/or stevia -- I usually use a combination. With the sweeteners, if using honey or agave nectar, you need to reduce the amount of liquids in the recipe by a little bit.
Chocolate - I replace chocolate chips with chopped organic 73% cacao chocolate bar.
Baking powder - As pp said, look for aluminum free stuff. I've also successfully replaced baking powder with baking soda in some recipes even though it's not supposed to be an equal substitute.
Other ingredients are probably a given -- use free-range eggs, use NT style crispy nuts. Since I make kefir cheese quite often, I try to use up my whey whenever possible by using it in place of liquids in my baked goods. I also find excuses to use shredded coconut, coconut milk, coconut cream, and coconut oil.