(covers information from several alternate timelines)
Freak was a derogatory slang term used to illustrate someone who had different attributes from other people.
In an alternate timeline 1944, Sal called the Na'kuhl Ghrath a "freak". (ENT: "Storm Front")
John Frederick Paxton considered Elizabeth a "cross-breed freak". (ENT: "Terra Prime")
In 2267, James T. Kirk called Spock a "devil-eared freak" to make him angry and counter the effect of the pod plants. (TOS: "This Side of Paradise")
In 2268, Spock was similarly called a "pointed-ear freak" by Achilles on 892-IV. (TOS: "Bread and Circuses")
Under the influence of the Beta XII-A entity the same year, Montgomery Scott named Spock a "freak" when the Vulcan had complained about serving with Humans. (TOS: "Day of the Dove")
Julian Bashir considered himself a "freak" because he was genetically-engineered as a child. (DS9: "Doctor Bashir, I Presume")
In 2369, Zayra, Morn and several other Bajorans formed a mob outside Constable Odo's office and called him a "shapeshifting freak". The group was calling him this because Odo was accused of murdering a Bajoran man named Ibudan. (DS9: "A Man Alone")
When stranded on an L-class planet in 2373, Odo and Quark started insulting each other; one of Quark's insults for Odo was "freak". (DS9: "The Ascent")
In 2380, Ensign D'Vana Tendi created The Dog, an artificially-created lifeform resembling a dog. Many of the crew referred to it as a "freak". When Tendi finally realized that dogs don't actually do what it can do, she called The Dog a "freak" as well, with The Dog already knowing it was one and just not wanting to upset her. (LD: "Much Ado About Boimler")