Stacks, of varying kinds, appear in algebraic geometry whenever we have moduli problems, most famously the stacks of (marked) curves. But these seem to be to be very geometric in motivation, so I was wondering if there are natural examples of stacks that arise in arithmetic geometry or number theory.

To me, as a non-expert, it seems like it's all Galois representations and estimates on various numeric measures (counting points or dimensions of things) based on other numeric things (conductors, heights, etc).

I asked this question at M.SE (here : http://math.stackexchange.com/questions/143746/stacks-in-arithmetic-geometry please vote to close if you can) because I thought it a bit too 'recreational', but with no success. What I am after is not just stacks which can be seen as arithmetic using number fields or rings of integers, but which are actually used in number-theoretic problems, or have a number-theoretic origin. Maybe there aren't any, but it doesn't hurt to ask.

EDIT: I have belatedly made this question CW, as I've realised, too late, that there is clearly not one correct answer.