Yuna, Rikku & Paine (Final Fantasy X-2); via the Dark Knight dressphere, Mascot, Alchemist, Blue Mage, Floral Fallal, Machina Maw & Full Throttle
Several Demons (Shin Megami Tensei III: Nocturne)
Several Demons (Shin Megami Tensei: Digital Devil Saga)
Shion Kozakura (Kagerou Project)
Azami (Kagerou Project)
Rider (Fate/Stay Night); via Mystic Eyes of Petrification
Uncle (Jackie Chan Adventures)
Daolon Wong (Jackie Chan Adventures)
Jafar (Once Upon a Time in Wonderland)
Yono the destroyer (Kim Possible)
Azami (Kagerou Project); via Staring Eyes
Shion Kozakura (Kagerou Project); via Staring Eyes
Boa Hancock can petrify any unlucky soul who falls victim to her charms with her Mero Mero Merrow.
Hideo Asou can petrify anything he touches.
Basilisx (Super Mario Bros. Z) can petrify anyone by looking at them.
The Grey Gargoyle (Marvel) can petrify anyone by touching them with his right hand, though the effect only lasts for one hour.
Anything Dabura (Dragon Ball) spits on turns to stone, as was Krillin's unfortunate fate.
Evergreen (Fairy Tail) using Stone Eyes.
Meta (Charmed) using her petrifying gaze (click for animation).
Serpentina (Power Rangers: Mystic Force) can summon many snakes (her "children") and when a victim is bitten by her snakes, she can activate her shield causing all who have been bitten to turn to stone.