I think Tobi has a third eye which is a sharigan on his forhead. His current mask hask has three eye holes and one of them is in front of his forehead. In Chpt.508 when Konan blew off half his mask, you can see he has bandages over his forehead. I think thats how hes his ghost-like abilities.
What do you think? That is all.
The idea that Tobi has more than two eyes is not a new idea. As we saw with Danzo, those eyes don't even need to be in his head: They could be on his arm, or on his torso, or on his legs. There are lots of parts of Tobi's body that we haven't seen yet in the manga.
We know he has a whole room filled with sharingan eyes in jars. You don't need to keep a room filled with spares if you aren't using them.
Hypothetically, Tobi finds an Uchiha with MS eyes with powerful space/time techniques like Kamui but at the next level. Tobi kills him and takes the eyes for himself, implanting them on his body in places to allow his body to be teleported to the other dimension and making himself intangible.
It's not a terrible theory, and it does explain why Tobi seems to have MS-level techniques (Super-Kamui and Tsukuyomi) without ever having displayed an MS sharingan in his eye hole. Even at times when people are passing through him and he's in the middle of using his space/time jutsu, his eye is still clearly a normal sharingan and not an MS one. That could be because he does have an MS, but it's somewhere else.