There is no such thing as ultimate ninjutsu,
but here are some of the strongest or more useful ninjutsus:
Edo Tensei (strenght depends on the number of edo summons the user has)
Dust Relese (not many ninjas are able to use this particle destroying technique)
Chibaku Tensei (gravitational technique that can crush almost anything)
Rasengan (and varieties including fuuton, an bijuu)
Susanoo (any version just comes with so many unique and strong abilities)
S/T Jutsus (this includes FTG and Kamui)
Great Shark Bomb (Kisame developed a jutsu that pretty much eats jutsus)
Amaterasu (the flames that never extinguish)
Chidori (and variations, under the right condition it can be used as Kirin a pretty dangerous jutsu)
that all I can think of right now.