Maria (Anima: Beyond Fantasy) use the corpse of the great beast of death and former messenger Memitim as a marionette, even being capable to use its necromantic powers.
Urahara Kisuke (Bleach) Bankai, Kannonbiraki Benihime Aratame, creates giant female bodhisattva puppet which he can manipulate by thoughts. Said puppet is also able to reconstruct and control anything it touches.
Pernida Parnkgjas (Bleach) extending its nerves via The Compulsory, allowing it to control anything they come into contact with, living or inanimate...
...allowing Pernida to control and twist its victim's body as it sees fit.
Zommari Rureaux's (Bleach) Amor can take complete control of anything any of his fifty eyes looks at.
Sheril Kamelot (D.Gray-Man) creating Dark Matter threads that can manipulate people's movements and bend them to horrible shapes.
Puppetmon (Digimon) can control other people's movements like a puppet through its strings.
Rappa Momochi (Gintama) controlling corpses as puppets to trick her opponents.
Machi (Hunter X Hunter) using her Nen Threads to manipulate her targets' movements.
Chrollo (Hunter x Hunter) stole ability called Order Stamp that allows him to affix stamp onto a "puppet" and control a large number of puppets by commands.
Ripple/Hamon (JoJo's Bizarre Adventure) can control people, as Jonathan used on Wang's headless carcass to disrupt the ships machinery and Caesar hypnotized a woman via kiss.
Noriaki Kakyoin (JoJo's Bizarre Adventure Part III Stardust Crusaders) demonstrates his Hierophant Green's ability to control his victims like a puppet.
Ganondorf (The Legend of Zelda) is skilled in puppetry, whether controlling Zelda or Puppet Ganon.
Screaming Mantis (Metal Gear Solid 4: Guns of the Patriots) uses puppets of Psycho Mantis and The Sorrow to control any living or dead person with Nano-Active Blood.
Kankurō (Naruto) is skilled in puppets, in both modification and usage.
Showing mastery in puppet controlling even in his childhood, Sasori (Naruto) was the greatest puppet master ninja of his generation…
…being able to summons an unprecedented 100 puppets, all controlled via his core.
Donquixote Doflamingo (One Piece) can use his String-String Fruit powers to bind parasite threads into hundreds of people's bodies controlling them like a puppet master.
With his mastery over his Straw-Straw Fruit/Wara Wara no Mi powers, Basil Hawkins (One Piece) can create and control the Straw Man, a demonic Voodoo Scarecrow.
Gein (Rurouni Kenshin) can use his diamond-filament steel wires to control his specially made puppets.
Alice Margatroid (Touhou Project) with her armed dolls.
Akabane Raishin (Unbreakable Machine-Doll) can perform martial arts while controling his puppet on fighting with little or no effort.
Puppeteer (Valkyrie Crusade) lives up to her name.
Puppetmaster (Valkyrie Crusade)
Kazuya Souma (Genjitsu Shugi Yuusha no Oukoku Saikenki) uses his magic, Living Poltergist to infused his conciousness into dolls or puppets to perfectly control them...
...such as his signature Musashibo a giant Sōhei doll...
...he can control Musashibo with such mastery to perfectly mimic the fighting skills of a master warrior.
Yura (Inuyasha) is capable of controlling people like puppets by using her hair.