1 Number One (Star Trek "The Cage"/"The Menagerie"): More than two decades before Captain Picard started referring to William Riker as "Number One," Majel Barrett filmed the original Star Trek pilot, where her character was known only as Number One. Like Riker, Number One was the Enterprise's first officer, but the novel Vulcan's Glory suggests Number One was her actual name, given to her because she possessed the top intellect of her planet's generation.
2 Number 5 (Short Circuit): Although roboticists Newton Crosby and Ben Jabituya were out to create artificial intelligence, they probably didn't expect any of their prototypes to suddenly gain sentience, and so assigned them numbers in lieu of names. But after prototype Number 5 becomes self-aware (and escapes the clutched of the US military), he decides that, as a living being, he should have a name, and calls himself Johnny Five.
3 Fifth (Stargate SG-1): One of the few characters with an ordinal number for a name, Fifth gets his name in a fairly straightforward manner: he's the fifth human-form Replicator to be created on the planet Halla.
4 V (V for Vendetta): Most people who live through encounters with the mysterious anarchist V think they're addressing him by a letter, and his propensity for using V-based alliterations when introducing himself seems to confirm this. But it's much more likely that V derives his name from the source of his vendetta; when he was subjected to medical experimentation at the Larkhill Resettlement Camp, he was the man in room five — marked with the Roman numeral "V."
5 Number Six (The Prisoner): Residents of the mysterious Village are known by a number rather than their actual names — including at least 16 individuals known only as "Number Two" — probably to protect the secrets they all inevitably carry. Number Six, the titular prisoner, protests in the opening that he's a free man, not a number, but it's implied that Number Six may be known by yet another number: Number One.
6 The Cylons (Battlestar Galactica): The creators of Battlestar Galactica have said that cylon Number Six is a tribute to The Prisoner, and it follows that each humanoid cylon model would have its own number, with the notable exception of the Final Five. Most cylon models are known collectively by a human name as well (the Sharons, the Leobens, the D'Annas), but individual Sixes tend to have individual human names, like Natalie, Caprica, Shelly, and Gina, perhaps because of they are so often used as infiltration agents.
7 Seven of Nine (Voyager): Names designate individuality, a concept the Borg have no use for, but sometimes it is convenient for the Collective to identify individual Borg drones. So when the formerly human Annika Hansen was assimilated into the Collective, she was given the designation Seven of Nine, Tertiary Adjunct of Unimatrix Zero-One. Even once she was unhooked from the hive mind, she preferred the shortened "Seven of Nine" to her human name, the latter of which she does not take up again until her Borg implants are completely destroyed.
8 Eight (The Specials): It's fairly obvious how Eight earned its superhero name. A hive mind, Eight consists of eight individual bodies who can physically act independent of one another, but share a single consciousness.
9 Thirteen (House): As long as we're labeling House as science fiction, we may as well mention Dr. Remy Hadley, better known as Thirteen. In one of his trademark moves to dehumanize his fellowship applicants, Dr. House assigned each applicant a number (and occasionally a humiliating nickname). Thirteen really took to the numerical naming system, refusing to divulge her actual name to her fellow applicants, and continuing to answer to Thirteen long after she'd earned a place on House's team.
10 Henchmen 21 and 24 (The Venture Bros): With the exception of the ill-fated Speedy, each of the Monarch's henchman is known only to their boss as a number. Henchmen 21 and 24 (the former is known to his mom as Gary) are genre-savvy enough to be content with their numerical positions in the Fluttering Horde. When they learn their new teammate is Henchman 1, they rightly assess that he's marked for death.
11 84 (P.S. 238): In a school filled with superheroes, Julie Finster has a pretty routine set of superpowers: flight, invulnerability, speed. In fact, her power set is so ordinary that instead of getting a cool superhero name, she's just called "84," since she's the 84th person to possess that particular grouping of powers. Needless to say, it's a tad demoralizing.
12 Agent 99 (Get Smart): James Bond may have been called 007 from time to time, but Agent 99 takes use of her code number to the next level, never answering to any other moniker (okay, in one episode, her fiance calls her Susan Hilton, but that isn't actually her name). In fact, she married Maxwell Smart and bears him twins without him ever learning her real name, proving once and for all that she's the better spy.
13 Agent 355 (Y the Last Man): In the historical spy network known as the Culper Ring, there was a female agent code named 355, whose identity has never been definitively determined. Similarly, in the fictional Culper Ring of Y the Last Man, Agent 355 is a highly competent spy whose name is never revealed (at least not to the reader). Her odd relationship with her name parallels that of Alter Tse'elon, the Israel commando whose real first name is not spoken (until the end) for fear of attracting the Angel of Death.
14 Experiment 626 (Lilo and Stitch): The alien mad scientist Dr. Jumba Jookiba created 626 strange and dangerous lifeforms. The wanton destruction caused by the final experiment, 626, condemns them both to life in exile, but the experiment escapes to Earth, where a young Hawaiian girl names him "Stitch." Of course, once Stitch's destructive nature has been reigned in, there are still 625 other experiments to contend with.
15 1812 (Farscape): In terms of numbered names, the DRD robot 1812 gets his from a fairly unusual source. Instead of 1812 being a serial number or a numbered designation, it's a reference to the 1812 Overture, which Crichton teaches the little service bot to play.
16 Subject 781227 (Kyle XY): Zzyzx, the company funding Adam Baylin's research, saw the child-shaped being Adam Baylin developed in his lab as a biological computer rather than a person, reflected in him getting a serial number in lieu of a name. It's only after 16 years, an escape, and a bout of amnesia that Subject 781227 finally gets a name: Kyle Trager.
