I also made pumpkin spice muffins and got these adorable edible "Santa Claus" and "Candy Cane" decorations. I made homemade cream cheese frosting, added multi-color sugar crystals and stuck the decorations on the top.
For the boxes, I always have a stash of fold-it-yourself boxes on hand in case we have visitors that want dessert, leftovers, etc. I stacked the cookies on one side of the box and put the cupcake on a folded "bed" of holiday tissue paper so it wouldn't tip over in transit. I got ribbon and gift tags at the 99-cent store (a completely madhouse during the holidays but worth the savings!), and even put a little "Pardon My Crumbs" sticker on the bottom left-hand side. Jon picked up the boxes tonight and was thrilled, even calling it his "fantasy holiday gift."
It was really fun and I hope I'll be able to do many more in the future. Hey, baby steps, right?