While I was disappointed that it was as "simple" as Neal being Bae as most had predicted, I still think the dialogue in his scenes (happily) indicates there's more to his story than that. Where has he been all these years?
I think the most popular theory is Neverland and that he will turn out to be Peter Pan.
But I'm still hoping/thinking he was in Wonderland and was in some way the White Rabbit. Why? First, the Hatters sign in his apartment. Second, the watches that he was trying to sell when he and Emma got into trouble. And finally all of his dialogue in this episode:
"The clock is ticking"
"You have three minutes."
That dialogue was very specific and repetitive. So I'm still voting White Rabbit.