What makes an S-ranked shinobi?
The ranking classification is mainly used for techniques and missions. For eg: "X is an A-rank technique" or "Y is a B-rank mission".

The ranks determine the difficulty or level of danger involved in the mission or technique mastering/usage. 

Out of the six ranks, only the S-Rank is used to classify a shinobi's class.


  S-rank is usually used to classify techniques intended for highly experienced jōnin and Kage-level shinobi. S-rank techniques are almost always unique to a single user, and as such are trademark abilities of that user.


Normally, S-rank isn't titled to Jōnin or Kage level ninjas. 


  "S-rank" is also a designation given to extremely powerful missing-nin, earning them a place in their village of origin's Bingo Book.


S-rank is used to classify only the most dangerous and powerful missing nins because of their level of skill, exceptional skill set and usage of (ultra) rare techniques.

So, for a shinobi to be classified as "S-Rank", they must have a unique and very powerful skill set and most importantly, they must become a missing-nin.



source: Naruto Wikia