Cults. Lots of cults.
I was always more interested in post-apoc fantasy not so much as a setting you put your players into initially but something you use to pull the rug out from under them and change the rules at a base level to see what happens and how the players react. I was considering running a heavy-magic campaign (I'm a slave to the FR, unfortunately) and having the players either witness or enact a cataclysm that either negates magic entirely or severely scales it back in the gameworld. I also considered making the players some of the few people who could still use magic post-cataclysm, in effect making them something like superheroes amongst normal men (even more than they already had been, heh).
Not so keen on actually using atomic weaponry from modern times, per se, but any analogue doomsday weapon would work. What about a fantasy bomb that, instead of emitting deadly radiation, semi-permanently alters the magic cast in its area into wild or dead magic? Think mythals.
Another cool idea would be, instead of taking the easy way out and throwing interdimensional Soviet scientists in with an atom bomb, you have the bomb actually discovered in the world. Say, for instance, dwarven miners come across a never before seen glowing substance that seems highly magical but sickens those who come into close contact with it. Then some malevolent group kills dwarves and seizes magic metal. PCs pursue the malevolent group not knowing what's afoot, and by the end of the adventure the malevolent group has built a dirty bomb / atomic device and detonates it. Or you could have somebody trying to use the weapons to kill Gods, or something.