WOW!! This is awesome!!!!
OH MY SWEET HOLY GRAHAM CRACKER!!! I second Cecilia's HOW DID I NOT KNOW THIS?!?!?
i don't know what's weirder, the history, or the fact that this discussion was right on top as i headed here to basically ask the same question.
I know I could read his backstory, like Joss' official one but I don't feel like spoiling the mystery. All I know is that he definitely is NOT going to the Special Hell and that's all that matters.
They made a comic about it now. It's called The Shepherd's Tale and reminds me of Memento. Well worth the read if not the purchase.
There's a comic book (weird) that explains it. Look on the Firefly Wikipedia page for the title.
I've always thought (and hoped) that he was an Alliance Operative similar to the one in Serenity, and either went rouge or has always been on some mission more complicated than we will ever comprehend.
I found a fan fiction continuation of the series that builds off serenity and the ending of the series that gives their explanation of who he is. I'm not sure if they used Joss's interpretation to create the episode or if it's their own idea, but I refuse to check because what they came up with is so perfect. Must resist checking wiki!