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 ostrich and tyrannosaurus of Earth, the M-113 creature (TOS: "The Man Trap"), and the Mugato of the planet Neural. (TOS: "A Private Little War")
Note that shapeshifters such as Changelings were bipedal when in humanoid form, but were not in their natural state.
Many of the highly-evolved life forms encountered by humans have remarked on their bipedal locomotion, including the Cytherian who contacted the USS Enterprise-D (TNG: "The Nth Degree") and the Caretaker, who referred to humans as a "minor bipedal species." (VOY: "Caretaker") Q Junior used the term 'biped as a (less than affectionate) term for humanoids (VOY: "Q2"). This suggests that evolving beyond the need for bipedal locomotion was a significant milestone in the evolution of a species.