Found this handy project by the California Academy of Sciences. They've 3D scanned many different kinds of skulls for everyone to look at- deer, whales, coyotes, bears, you name it. They are interactive, so you can rotate and/or zoom in and out. Looks like a very useful source if anyone needs a reference for drawing animal skulls!

Additionally, here's a link to a 3D museum, which has models of mammal skulls as well as birds, and a couple fish.

edit 8/6/17: added another link

edit 10/17/16: updated link, the original website doesn't seem to be available anymore?