Madara's MS techniques.
O.k. I don't know if this will make sense or not, but do you think that Madara's ability to appear, and disappear is one of his 3 MS techniques?
First, I want to say that ability may be his best ninjutsu(Just like Ametarasu was Itachi's). When he appears in the latest manga, it is with his right eye:
Naruto 453 page 01 | One Manga
This may signal that this is his best ninjutsu, in that it has been previously said that the right eye of the MS contains powerful Ninjutsu:
Naruto 389 page 01 | One Manga
The only exception is Kakashi, as his Ninjutsu is in his left eye. However, that may be the only technique kakashi can use. (With his MS)
Crappy theory, :p but whaddya think? (Not even a theory, just wanna see what you guys think...)