You Are Number Six/Web Original

Patient #11 from Lonelygirl15 season 2, and Patient #12 from Kate Modern: The Last Work. Both have names that are eventually revealed, but since the Order regard them as nothing more than test subjects, they refer to them only by their patient numbers.
The Angels of Open Blue take after Halo's Spartans in their naming conventions.
Every single character in Survival of the Fittest has a number assigned to them by the terrorists. Their real name and number are often used in conjunction, although Bobby Jacks was once refered to explictly as 'B06' (the letter denotes gender).
Two from Tales of MU, who named herself for what the runes on her forehead spell.
Subject Five of Unlikely Eden, named because she was the fifth subject of a preliminary eugenics project.
SCP Foundation: All catalogued SCPs are referred to by number whether or not they're human/sapient, in order to avoid becoming too close to Reality Warpers and other people and things of mass destruction.
Patient 4479 in The Joker Blogs is referred to only as—well, Patient 4479. He refuses to or is unable to supply his real name, and the majority of characters would rather call him 4479 than Joker.
Seven in Off White. Though it's not for dehumanizing purposes. She just hated her real name.