Freeze cookies before or after baking them?
If the oven time is not a limiting resource, I would freeze and then bake. 

There are a number of sources that strongly advocate for aging cookie dough before baking, which affects the absorption of moisture in the dough and changes flavor:
http://www.nytimes.com/2008/07/09/dining/09chip.html

Personally, I normally do not have the patience for aging dough. If I am making cookie dough, I want to bake it and eat it immediately. You, however, have the time built in to age your dough before baking. You may even want to leave the dough in the refrigerator for awhile first before freezing. 

Also, I think cookie freshness suffers more after baking than before, but I don't have references for that.