So I did both. I baked some cookies, attached the ingredients for the recipient to be able to recreate and then I got a little crafty.
With a basic hand stamping set purchased as a deal on Pick Your Plum one day, I stamped the word "Cookies" onto a mini cookie spatula (pretty sure I found them at the dollar store). You then use a Sharpie to trace the inner embossed area to make it little easier to read. Voila. Cookie gift basket.
You can find the hand stamp letters here: http://www.harborfreight.com/3
And the instructions for layering cookie in a jar recipes here: http://allrecipes.com/Recipe/C
I simply used mini chocolate chips and an extra 1/2 cup of mini M&M's in my cookies, because, well I had them on hand. :)