As the "leader" of the Nagato fan base, I can conclusively state the following characters (for their reasons beat Nagato; besides the obvious Madara and Hashirama) :
1. Mangekyou Obito - Possesses Kamui, for which Nagato does not have a counter for at all (as the two known counters are the opposite Kamui and a mobile FTG, which only Minato and Kakashi possess) immense will power, Mokuton, Inyouton abilities (the ability to create out of nothing) some of the best Genjutsu in the manga, Juubi sized Katons, immense speed etc. Too much for Nagato to handle in one go. The fight will end with Obito catching Nagato off guard and subsequently warping him.
2. Bijuu Sennin Modo Naruto - Naruto possesses WAY TOO MUCH firepower for Nagato to fully handle him. Immense speed for which Nagato most likely can't react to (it's like Karin's sensing, not Sage mode's combat sensing), various Rasengan variations, Bijuudama etc. The Bijuudama especially is a bane for Nagato. Naruto can infuse Senjutsu in to it, more than enough needed that will turn Nagato to stone and the time it will take Nagato to absorb it will give Naruto an easy opening to Shunshin behind Nagato (being arguably the fastest Shunshin user in the series) and engage in Frog Kata, to which not even Preta enhancements will be able to tank.
3. Eien No Mangekyou Sharingan Sasuke - Perfect Susano'o in conjunction with Enton is WAY too much for Nagato. Not only does Nagato need to be wary of the constant spam of various Enton which will keep him on his toes, various slices from Sasuke's PS sword will end Nagato before he can engage in any form of combat. Sasuke's massive Susano'o also allows him to eradicate the massive ball create from Chibaku Tensei.
4. Bijuu Modo Minato - He is essentially a supercharged version of Bijuu Modo Naruto, who Nagato is pushed to High difficulty to defeat, but with the added benefit of: 1. Hiraishin and its variations 2. S/T Barrier to negate any projectile based attack Nagato uses 3. Reflexes that will never let him get caught off guard by Nagato 4. Bijuudama which will work in a similar fashion to Naruto's way to win with this method. But even better given that he will be INSTANTLY behind Nagato and will end him before Asura's enhancements take effect. He also has the benefit of creating a Sage Mode clone before hand and can have it use FTG behind Nagato while he bombards him with the Bijuudama.
Everyone else down the top 10 list loses to Nagato.
