The Sacred Jewel of Four Souls (Inuyasha/Inuyasha: The Final Act)
Wish Tickets (Majimoji Rurumo)
Wish-Granting Ring (Mermaid Melody Pichi Pichi Pitch)
Brew (Soul Eater)
The Dragon Balls (Dragon Ball), via Shenron or Porunga
The Star Rod (Paper Mario)
THE BROWNSTONE SPIRE (Welcome to Night Vale)
Chaos can grant his own wishes without limitations. Making this power at it's full potential a variation of reality warping.
Crossroad demons (Supernatural) can grant the wishes of humans, but said wishes always result in the demon claiming said human's soul.
Shen Long (Dragon Ball) can grant three wishes of anyone who gathers the seven Dragon Balls, under certain limitations.
Porunga (Dragon Ball) can grant three wishes of anyone who gathers the seven Namekian Dragon Balls, and have been powered up to exceed its former limitations.
Ultimate Shen Long (Dragon Ball) can grant one wish of anyone who gathers the seven Black Star Dragon Balls, and is so powerful that it seems little to no limitations exists for it.
Vengeance demons (Buffy the Vampire Slayer) grant vengeance-related wishes of anyone who says them, though said wishes often result in the victim's gruesome death or even the creation of alternate realities.
Kyubey (Puella Magi Madoka Magica) can grant wishes in the form of contracts which result in the wisher becoming a Mahou Shoujo. Unfortunately, these wishes usually backfire in ways that drive the wisher to despair.
Jirachi (Pokemon) can grant any wish to anyone! Even if the wish is...
A big pile of candy and snacks!
Bey Blade (The Secret Magical Gourd)
The Hogyoku (Bleach) can manifest the user's desires based on the strength of the user's Reishi.
Brew (Soul Eater) can manifest the user's desires based on the strength of the user's soul wavelength.
Mephistopheles (Valkyrie Crusade) is a demon lord with very powerful and unique alchemy and magic and posses the power to grant any wish.
Experiment 267 "Wishy-Washy" (Lilo & Stitch)
Wyrm (Teenage Mutant Ninja Turtles; 2012 TV series)