this is a hard one... if what Tobi said is true that he "Gave" nagato his rinnegan then we have not seen the extent of what Tobi can actually do with it.
Madara showed he can use the techs that Nagato used (at least some of them so far) but also brought down Freaking meteors to smash earth.... pretty boss if you ask me...
Nagato had mad skills and revived thousands of folks he killed so that is pretty bad a if you ask me....
My pick is Tobi (flame me if you want) and here is why.....
if you believe he gave Nagato the rinnegan then you have to believe he had it and used it and probably was involved in teaching nagato how to use it.... He also controlled 6 former Jinchuriki and put them into full tailed beast mode and did this with 1 freaking rinnegan which would have to take a HUGE ammount of chakra to do so. Also The fact that he chose not to use both rinnegan tells me that he knows more than everyone else about the rinnegan, that he is bad A and that he has not shown us near his full capabilities....
My main arguement for Tobi is that since he can use sharingan and rinnegan at the same time, he is better then the other two users. Tobi can use 1 sharingan and 1 rinnegan at the same time which makes his use of the rinnegan that much more dangerous.
Oh yeah.... the fact that he has not had to use Any rinnegan techniques yet even though he is fighting against BM Naruto, Super Kakashi, Gai, and Bee in 8 tails mode tells me that his rinnegan abilities must be pretty bad ass... because at this point the skills that nagato and Madara showed with the rinnegan would get him owned if he tried to use them.