Part of what makes Naruto so great is the startling array of incredible powers that the characters possess. Among the most interesting are kekkei genkai, techniques that are unique to one person or family. These abilities are sometimes created by combining elemental release techniques - for instance, water and wind can be combined to create ice release, a kekkei genkai used by Haku. Others are inherited abilities based in the eye, like the sharingan, byakugan, and rinnegan. Still, others are random mutations that have no apparent basis - Kimimaro's ability to manipulate his bones and wield them in his own defense is one of those.
The best kekkei genkai users include legendary powerhouses like Madara Uchiha and Hashirama Senju, as well as the protagonists whose growth you get to observe over time, Naruto Uzumaki and Sasuke Uchiha. Who is truly the top user? That's up to you to decide.
Hashirama's wood release kekkei genkai was considered so impressive that Orochimaru slayed 60 children in an experiment intended to replicate it. Wood release allows the user to create plant matter, specifically trees. He actually created the forest that Konoha was built on, which is part of why he became the first Hokage.
The technique can do a whole lot more than just create trees, however. He can create functional wooden clones of himself, create houses and other complex structures made of wood, and even suppress the chakra of tailed beasts.
Itachi Uchiha was considered one of the most powerful living members of the Uchiha clan, which is why he was chosen by Danzo to slay the rest of the family. What makes him so powerful? It's his kekkei genkai, the sharingan. This eye-based power allows users to use a variety of incredible techniques - most notably, he can copy any jutsu used by another person. After witnessing his friend Shisui take his own life, he awakened his mangekyo, the next stage of the sharingan.
With one eye, he can use Amaterasu, which allows him to produce a fire that never goes out. With the other eye, he uses Tsukuyomi, a genjutsu that distorts the targets ability to perceive time. He can also use Susanoo, a nearly impenetrable defense that takes the form of a giant glowing skeleton.
Madara is one of the most powerful ninja in Konoha history, and he doesn't slack off in the kekkei genkai department. Starting life with the sharingan that's common to the Uchiha family, he later awakened the mangekyo shaaringan, which only appears after the user experiences severe trauma.
Later, through splicing his DNA with Hashirama's, he was able to acquire both the rinnegan and wood release - and he can use storm release, too. Even just one of these kekkei genkai would make him into a terrifying opponent, but with all five it takes an almost godlike ability to even put a scratch on him.
Though not the only person to possess a rinnegan, Nagato, also known by his nickname Pain, is one of the most noteworthy. Through the rinnegan, Nagato is able to use the Six Paths Technique, which involves a wide range of incredible abilities. The one that Nagato focused on the most was the Outer Path, which gave him control over life. Nagato was able to reanimate a group of lifeless bodies and use them as a proxy for his own, forcing the proxies to fight his opponents while he remained in a safe location.
Though he was ultimately defeated by Naruto, he almost wiped out Konoha before he was taken down.