Sigil Stones are specially prepared Morpholiths used to open Gates to oblivion. Since it is no longer possible to open a permanent gate to Oblivion, and since, once a gate is activated, the sigil stone used to create it is transported to the place in oblivion where it's sigil was inscribed, it's incredibly unlikely we would see them.

I could see one or two being rare items/easter eggs, but yeah in general I doubt we'll see the Sigil Stones return in any vast quantity.

So I take it dragon shouts are going to be those special items we get for destroying a tough enemy, like the sigil stones in oblivon.

I guess that's one way to think of it. Oblivion gates are to Dragons as Sigil stones are to Dragon shouts. That is, if that's how dragons will be treated n Skyrim. I hope they are less temporary than Oblivion gates.