I have a 2 year old that loves Sunday School. Each week for their craft they find new ways to "color" their coloring page for the week, and she never gets tired of it. I find that the younger ones learn a lot from a picture of the story they are learning and this is a great way to make an easy craft when you have no ideas.

Washable markers
Finger paints (make sure they're wearing a shirt over their clothes)
The some paint recipes and ideas check out the Sunday School time fillers page.
Glitter glue
Stickers
Chalk (spray with hairspray after so the chalk won't rub off)
Fun foam with shapes that apply and glue them on
-Valentines Day use hearts
-Samson and Delilah use scissors and comb shapes, etc.
stamps or marker stamps