My theory is that Tobi is Izuna, Madara's younger brother.
There's a little clue I think in Chapter 490 after Kabuto resurrects the dead Akatsuki. Here's the quoted dialogue from that scene:
Tobi: "You want to join forces... What's in it for me?"
Kabuto: "You're planning to start your war very soon... I can bolster your fighting power: With Itachi, Sasori, Deidara, Kakuzu, and Nagato."
Tobi: "What do you want in return?"
Kabuto: "I need Sasuke to answer my questions. A fragile, living Uchiha."
Tobi: "And what if I say no?"
At this point, Kabuto resurrects someone else who is later revealed to be the true Madara. Tobi shows fear at seeing Madara's face.
Tobi: "Th-that's..."
Kabuto: "Did you really think I'd extend my hand without a back-up plan? You cannot refuse me!"
Tobi: "You madman... How did you do this?"
Kabuto: "Oh you know... Anyway you can relax. I haven't told a soul."
So at that point we can pretty much assume that Kabuto does in fact know who Tobi is, and that Tobi has some kind of relationship with Madara which makes Tobi fear him. When Izuna was younger, Madara stole his eyes so he could have Eternal Mangekyou Sharingan. Wouldn't that make him have some fear for his older brother? I don't know, that's my reasoning.