As far as we know, Anakin appears to have the following injuries. 1) Severed Arm 2) Breathing Problems 3) A large gash to his head The Severed Arm, as we know, came from Dooku chopping it off and we saw later that he obtained a robotic one. The breathing problems and the large gash to his head will be received in Episode 3. However, how he received it is a complete mystery. We can't be for certain that Obi-wan tore his lungs and his head up during their climatic battle over a Volcano. It just wouldn't seem like Obi-wan to tear up his own apprentince regardless of how much hate has consumed Anakin. Perhaps it was more of an accident then anything. Maybe at some point in their duel, Obi-wan pushes Anakin over the side of a volcano or some molten pit. Anakin receives a gash on his head from the fall, and get his breathing problems from all the smoke inhalation from the volcano smog. Obi-wan has his famous quote, "He is more machine now than man." But it could be more of a symbolic reference than something meant to be taken literally. Anakin is a cold, heartless and souless individual. More than likely Vader, has 90% of his body still intact.