In a teaser trailer for Diablo 2, found here:
http://www.youtube.com/watch?v=kVv41NarVP4,
you see the Dark Wanderer sitting at the back of a wagon talking about what has happened since he left Tristram. He is holding Diablo's soulstone in his hands, but the trailer ends with him throwing it away and leaving it in the mud.
When next you see it, it is embedded in the forehead of Diablo, when you fight him in the game.
If he needed it, why did he throw it away?
My thought is that it's not the same stone. I don't think that you have destroyed Diablo nor his soulstone. Maybe he got his hands on another stone, the stone that you see smashed in the cinematic, in order to pretend to die, but actually live on. This could explain him being i Diablo 3.
I don't know if the trailer is considered canon, however, but in any case, let me know what you think
Droezd
(Also, if this has already been covered on the forum, I apologise.)