"When you are through" is derived from the American-ism of being "through" with something. But would more normally imply position or movement, e.g. "Superman flew through the air", "Push the trolley through the shop".
In British-English one is not through with it but "done with it" (informal) or "finished with it" (more proper)
"Done" is considered less correct but is in common usage, I think, again, it may be an earlier American-ism, though I am not sure.
So to conclude; "When you are finished" is the best version, though Americans will also use the other two phrases interchangeably.
EDIT: "When you have finished" would be better again