Actually Christmas "spice" type cookies do really well with honey instead of sugar. I bet you could find some good recipes.

That was our "homemade" gift that the kids could participate in. THey helped me roll and cut gingerbread cookies, decorate them (but they'd be fine plain), and then I wrapped a pretty ribbon around a grapevine wreath, and tied the cookies to the wreath. It turned out super.

If you have gifts for family members from yourself, your sons contribution could be the wrapping paper. You can use plain newsprint, and make stamps for him out of potatos. We use acrylic paint for that and it's pretty neat.
There are now wax decorating pens that you can use to decorate candles, he could do something like that.
ETA, the other thing I want to try with my kids is cinnamon ornaments. Non-edible, but they involve the same rolling and cutting as cookies. You could even put them on a wreath like I did with the cookies.