From the ArcaMax Publishing, Gardening Newsletter:
http://www.arcamax.com/news/gardening/s-156675-893710
Question: Something is digging up my yard at night. Any idea what it
is?
Answer: It's difficult to know exactly who the culprit is; it could be
a skunk. Skunk activity seems to be higher in the spring and then
lessen naturally, so the problem may stop all on its own. Skunks may
present a health hazard (if rabies is in your area or if they are
feeding in trash cans, etc.) and so I would suggest you contact your
local animal control agency for assistance with skunk problem. Other
possible culprits include moles, voles, gophers, and squirrels.