Princess Valkyrie (UFO Ultramaiden Valkyrie); via Key of Time
Time Wizard (Yu-Gi-Oh!)
Wizards (Diablo 3) have the innate ability to cast several time-based spells.
Dimaria (Fairy Tail) in her Chronos form casting Age Scratch, a time-based spell that allows her enemy to regain all the injuries it sustained and healed up to the present point of time.
Ultear (Fairy Tail) is a prominent user of the Arc of Time, a magic that allows her to manipulate the time of objects, rewind time and enhance/strengthen people with powers gained from their own future.
Time Mages (Final Fantasy) are adept users of Time Magic, allowing them to slow, stop, or freeze enemies, fasten the speed of allies, manipulate gravity till a certain extent, and call upon the power of certain celestial objects to damage enemies.
Mages (World of Warcraft) through the Arcane school of Magic have the ability to cast spells like Time Warp.
Perse (Valkyrie Crusade) is an time mage.
Racer (Fairy Tail) making great use of his Slowing Magic, a time-effecting magic that alters the perception of time from his opponent's point of view
Morgana (Marvel) used magical time travel frequently.