With the canonical death of Warhammer Fantasy, some alternate scenarios have come up, either altering minor aspects of the history, to radical reimaginings. This page is a stub, but feel free to expand more on this.
Bow of the Prophet
Bow of the Prophet's core premise is: What if The Empire were based off the Ottoman Empire instead of the Holy Roman Empire? To read about it, go here The outline for the setting, if you want to contribute with the original authors, is here.
Warhammer End Times: Grom
Created by Kevin Coleman (author of the Gnoblar Horde army for 6th) as a supplement for The End Times, this setting works on the premise that Grom did not perish at the hands of Eltharion the Grim, but becomes the Incarnate of Gork and Mork. Contains updated rules for the Gnoblar Horde, Grimgor'z Ardboyz, Waaagh! Grom, the Hobgobla Khanate, Morhog's Horde (Black Orcs that have enslaved Chaos Dwarfs in an ironic role reversal), and the Snotling Army. Check it out for a larf.
The End Times ends in the mother of all stalemates. Karl Franz and most of the Elector Counts are dead, Archaon perished, and the Skaven have descended into all the petty infighting. Now everyone's desperately trying to put together all the pieces, with the legions of Chaos eagerly awaiting the coming of the next Everchosen...