You Are Number Six/Film

"Radio: Calling B4; come in, B4; why don't you answer, B4?' Bluebottle: Because I didn't hear you before!"
 * Dr. Zin's Mooks 425, 426 and 427 in Jonny Quest vs. the Cyber Insects. They wear uniforms with numbered tags instead of names. No word on what happened to 1 through 424, but given Zin's tendency to punish the tiniest slipup with death it's easy to guess.
 * 9 even has nine numbered protagonists.
 * B4, progenitor to Data from Star Trek: Nemesis. This is, of course, a play on the fact that B4, being a prototype, came "before" Data and is, in fact, lampshaded by Picard in the offhand comment: "Dr. Soong's penchant for whimsical names seems to have no end."
 * Or, as an old Goon Show joke had it:

""Red five, standing by.""
 * Star Wars:
 * All the droids go by their model numbers. The funny thing about the droids is that they grow more 'human' as time goes on, so the number becomes just like a personal name; in fact, Expanded Universe convention spells the numbers out phonetically in dialogue, not necessarily using the spellings of the individual digits. R2-D2 and C-3PO are normally referred to as Artoo and Threepio.
 * Stormtroopers. "TK-421, why aren't you at your post? TK-421, do you copy?" In the novelization, the trooper's number is THX-1138.
 * Fighter pilots are also given numbers, which they are supposed to (but don't always) use on the communications broadcasts, to preserve their identity in case their encryption gets broken and the enemy intercepts their transmissions. This is seen mostly in the X Wing Series and other series that feature fighter pilots, but shows up in other places as well, including the movies.

""Then I saw him--the Man from Room Five.""
 * Clones were given their production numbers as their names, resulting in a series of letters and numbers as their "official" names. The Jedi were more understanding, and most of them allowed their clone charges to have nicknames, both for the ease of identification and for individuality. Sadly, after Revenge of the Sith these were all but obliterated.
 * Alex in A Clockwork Orange is known only as "six, double-five, three, two, one" while in prison.
 * Sanjuro from Yojimbo gives himself a number-name due to the fact that "I'm about 36 (san-3, ju-10 ro[ku]-6) years old." His other name is due to the grove of mulberry trees he happens to be looking at. Yay, sericulture.
 * Everyone in THX 1138.
 * The two brothers running the restaurant in Big Night are Primo and Secondo, Italian for "First" and "Second" respectively.
 * Done in a slightly cryptic way in The Matrix series, with Neo (identified as "the one" and also an anagram of "one"), Trinity, and Cypher (one somewhat esoteric definition of cypher (also spelled "cipher") is the digit zero; it comes from the Arabic word "sifr", which means, well, zero. Technically "zero" also comes from "sifr", but that's a whole other matter).
 * In The Animatrix, it is mentioned that the machines named their city "01".
 * The robots in Short Circuit were all named after numbers. Somehow, Number Five acquired sentience, and changed his name to Johnny Five.
 * In The Island, the clones have a sort of mix of this. A clone's first name is the last name of his or her sponsor, which is followed by a number and code for a letter (the protagonist is "Lincoln 6 Echo") to denote what "series" of clones they're from. Notably, the antagonist keeps calling the protagonist "Six Echo," instead of "Lincoln".
 * The title character of V for Vendetta (it's a roman numeral).

"Everything is numbered here."
 * The superhero "Eight" in The Specials is a Hive Mind controlling eight human bodies.
 * One Two from RocknRolla.
 * The title character of Ben-Hur is known as "Forty-One" while onboard the Roman galley.
 * In Invasion of Astro Monster, the aliens from Planet X refer to King Ghidorah as Monster Zero, Godzilla as Monster Zero One, and Rodan as Monster Zero Two.


 * The brothers in Stardust who kill each other off for the throne and then hang around as ghosts to see who gets it were apparently bred expressly for this purpose, so that whoever should inherit should have earned it by cunning and strength. They were therefore named impersonally, with Latin names designating their birth order, Primus to Septimus.
 * Worker 11811 (or Georgy), who Freder "trades lives" with in Metropolis.
 * Weapon XI in X Men Origins Wolverine.
 * In Austin Powers, we have Dr. Evil's henchman Number Two, and The Mole, Number Three.
 * The above is a reference to the James Bond movies, where members of Blofeld's organization are known by numbers, including Number Two (Thunderball) and Number Eleven (You Only Live Twice).
 * Number Two is actually his name, for he's Dr. Evil's number one.
 * A variant occurs in the beginning of Wedlock, where all the prisoners are assigned colors as identification, and have to use them instead of their own names.
 * The jurors in 12 Angry Men are referred to only by juror number (the film ends with two jurors introducing themselves to each other, but this was not in the original play).
 * Toward the end of The President's Analyst, the title character is abducted by  who intend to extract information from him to help them secure legislation to   and substitute numbers for names as the only legal identification for efficiency.
 * In Ultraviolet, Violet rescues a young boy from the clutches of the Big Bad, who is believed to be the boy's father. When Violet asks the boy what his name is, he responds by holding up six fingers. Later on, the Big Bad reveals to Violet why Six is known as such:
 * Just Imagine (1930). In the amazing future of 1980's New York, everyone has an alphanumeric name like J-21.
 * The Mothman Prophecies. "Wake up, number 37."
 * In non-English markets, Buster Keaton was often given a local nickname that meant "zero" or "the hole in a donut."
 * The names of the three sons of daimyo Hidetora Ichimonji in Akira Kurosawa's Ran—Taro, Jiro and Saburo—actually mean "first boy", "second boy" and "third boy" and are popular Japanese first names.
 * I Am Number Four plays with this. It's averted in that the numbers are not actually used for names, but as target designations. However, it's deliberately invoked in Number Six's case, who identifies herself as "Number Six" (except one snarky comment to Sam that her name is "Jane Doe") and refers to John only by his number.
 * The Don in The Finger Points (who is clearly based on Al Capone) is referred to only as "Number One"—even in newspaper headlines.
 * "Eight" from The Specials, so named because (s)he is a Hive Mind inhabiting eight human bodies.