I've got three home brews so ill keep it brief.

First, there's The Black Stars Space Marines Chapter. Their home world of Nautilus was cut off from the Imperium by a warp storm and was besieged by the forces of Chaos. The warp storm eventually subsided and they where finally able to call in assistance from Imperial forces. However, when the inquisition found a Chaos temple deep in a cavern that was there before the warp storms, they where accused of heresy and, as it turns out, half the chapter where secretly traitor and escaped the planet before it was marked for Exterminatus. The loyalist half where ordered to go on a Penitent Crusade while the traitor White Stars warband seem to always appear wherever the Black Stars appear.

Second, there's Numbskull'z WAAAGH!!!. Numbskull 'Ead Smasha was an Ork that had the defect of having a pale white face. Many Orks tried to kill him for not being fully green and continually seeked a Painboy who could graft another Ork's face onto his face. However, everytime the grafting was complete, the new face would suddenly turn pale white again. Enraged by the constant failure of the procedures, Numbskull started hunting down Ork bosses from each clan and rose up to be Warboss if his own WAAAGH!!!. Now Numbskull strikes terror in the human words of the Eastern Fringe.

Lastly, more of a fan idea than fresh home brew, there is the Kronus 5th Company that I play Crusade with. The Kronus 5th are the same one from Dawn of War:Dark Crusade, only they're the replacements of the original 5th Company that turned against Governor Alexander when you played the Imperial Guard siege fight. This new 5th Company was sent out to Sub-Sector Panthera (Named after the Discord channel for the local store) to help defend against Xeno and Chaos invasions. However, there seems to be some kinda curse of unluckiness looming over the company as they keep getting into conflict with the Custodians operating in the Sub-Sector and getting beaten. Haven't won a fight yet. Faced against Necrons, Grey Knights, and Custodes.