A biped was any organism which used two limbs as its primary means of terrestrial locomotion. Types of bipedal motion included walking, running, or hopping, as long as only two appendages (usually called legs) were used.
While the term biped could generally be interchangeable with the term "humanoid," this was not always the case. Most humanoids are bipeds, but there were many non-humanoid bipedal species, including the Tyrannosaurus rex of Earth, the Gunji jackdaw (DS9: "If Wishes Were Horses"), and the Mugato of the planet Neural. (TOS: "A Private Little War")
Shapeshifters such as Changelings were bipedal when in humanoid form, but were not in their natural state. (DS9: "The Search, Part I")
Many of the highly-evolved lifeforms encountered by Humans have remarked on their bipedal locomotion, including the Cytherian who contacted the USS Enterprise-D and the Caretaker, who referred to Humans as a "minor bipedal species." (TNG: "The Nth Degree"; VOY: "Caretaker") Q Junior used the term "biped" as a (less than affectionate) term for humanoids. (VOY: "Q2")