What changes brought about by the war had the most effect on civilians in both the south and the north?

The freeing of the slaves. They were actually worse off after the war than before. The great irony of the civil war was that it was coming to the point where the landowners could not afford to buy and use slaves economically. Had the north waited, the south would have had to find another way to farm their land.

When the war ended the slaves were free to go anywhere. The north took advantage of this and paid them barely enough to live. They were free, but they were economically still enslaved. 

You can find out this by reading about the problems of reconstruction. Just google problems of Reconstruction.