I read once from a biography of a Romanian ex-KGB agent that it was common knowledge inside the KGB that Arafat was a homosexual. He said in his biography that he always wanted to fiercely was his hands after meeting with him, I suppose because of this fact/rumor. I've heard further rumors that he was a pedophile, but those are less substantiated.
Obviously, there are other ways to get AIDS, but if the above is true, it makes you wonder if perhaps it wasn't AIDS.
I'd also heard Arafat had parkinson's disease, but I don't think that bears on the circumstances of his death.