1. Uchiha and Senju
The Uchiha and Senju Clan were always even during the war era. Whenever the village hired Uchiha, the other would hire Senju and vice versa.
Relatives to the Senju so they had blood relation to the Sage of Six Paths. They were chakra beasts and only them were capable of hosting the nine tails. And they specialized in fuinjutsu which I believe is the most dangerous type of jutsu. This alone made them fearful.
3. Sarutobi Clan
Third Hokage, Asuma, and even Konohomaru are good shinobi. They can master high-level techniques easily. Konohomaru learned an A rank jutsu younger than Naruto, and Hiruzen was "God of Shinobi."
4. Hyuuga Clan
I put this clan at number 4 because Neji is the only member of this clan that lives up to the hype. Hinata just hasn't got any shine at all. All members born into this clan possess the Byakugan, a kekkei genkai that gives them extended fields of vision and the ability to see through solid objects and even the chakra circulatory system, amongst other things, and expel chakra from any of the tenketsu in their body.
5. Juugo's Clan
Juugo's clan had the ability to absorb natural energy from there surroundings. This ability was interesting enough to catch the attention of Orochimaru.
6. Hozuki Clan
This clan has the ability to liquify their bodies. Members of this clan are Suigetsu, Mangetsu, and the 2nd Mizukage. Suigetsu is a skilled swordsman and Mangetsu was one of the most powerful members of his village. Being capable of wielding all the 7 swords.
7. Aburame Clan
A noble clan of konoha that's able to use insects as weapons. Torune was a high level shinobi that Danzo believed would be a good bodyguard. Him and his dad are the only ones known to have nano-sized, venomous insects.
8. Akimichi Clan
9. Nara Clan
10. Fuma Clan