This question annoys me to no end.
I always want to say Scar because he didn't kill Nala, as is customary when a new lion takes over the pride. But then again, it could be Disney refusing to kill the future Queen, so it could just as likely be a rogue Sarafina met, fell in love with, and one way or another after they mated he disappeared.
Although, I highly doubt it was Mufasa. Having Simba and Nala related by doing a Scar/Sarafina pairing is enough, but I think parents would flip out if they found out Simba married and had a cub with his step-sister.