Jok has an amazing book called Sudan. It is out of print and was written before many of the more recent developments (07) but it provides a great framework and i cannot recommend it enough.
I like The First Sudanese Civil War: Africans, Arabs and Israelis in the Southern Sudan, 1955-1972 by Scopas S.Poggo.
The author was born in the Southern Sudan in 1960 and attended the University of Juba. Furthermore, his father and mother were both involved in the Anyanya movement, both in Southern Sudan and as refugees in Uganda.
These factors certainly give the author a viewpoint on the war; but I feel he does an admirable job of presenting a comprehensive and sober treatment of the events.
I really liked "What Darfurk? An Unbiased Book on the Two Sudanese Civil Wars".