A mistake or shortage of ingredients isn't the only reason you might consider a substitution. Sometimes I consider a substitute ingredient when a recipe calls for a very small quantity of something I don't normally stock in my pantry, or to replace an expensive ingredient. I'm very adventurous with substitution in cooking- sometimes out of necessity, and sometimes just for fun!
I'm more cautious, however, about ingredient changes in baking. Baking results are much more dependent on texture and chemical reaction. The Joy of Baking's recommendations make sense to me, based on what I have learned about baking, but I have seen some resources that I wouldn't trust.
So, use the "mise en place", a French phrase meaning "everything in place". If you still need a substitution, give one of these lists a try!