Time Lords/Timestresses (Teenage Mutant Ninja Turtles)
Dialga (Pokemon series)
Nayru (The Legend of Zelda: Oracle of Ages)
Ambi/Veran (The Legend of Zelda: Oracle of Ages); via completing the Black Tower
Anachronos (World of Warcraft)
Nozdormu (World of Warcraft)
Chronos (Valkyrie Crusade)
Time (Alice Through the Looking Glass)
The Time Cops led by Time Baby (Gravity Falls) act as the official governing body over the laws of space-time.
Chronos (Valkyrie Crusade) the goddess of time.
Subaru (Saint Seiya Ω) is the human body of Saturn, the god of time. He can subjugate any chronokinetic power, like the time stopping. Subaru could remain conscious after be frozen in time, and could hurt Tokisada even when his body managed invulnerability.