In real life, most people have very common and completely ordinary names. But not so in fiction. If a character is to have any relevance to the plot, he has to have a name that sounds either cool and tough, or ominous and evil. But sometimes they don't. Everyone else does, but not these characters. Their names are just so ordinary and common that it really sticks out.
This trope is the middle ground between Awesome McCool Name and Unfortunate Names. Compare with Aerith and Bob, when characters with completely made up names appear side by side with others that have completely mundane names. Might overlap with Mr. Smith if the name has been selected deliberately. See also Fluffy the Terrible, Tom the Dark Lord, Sesquipedalian Smith, Some Call Me Tim, and Odd Name Out.
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Anime and Manga
In Elfen Lied, the massive, floating head, Body Horror oracle that is kept in the pool under the research facility is just called "Anna." Helps that she was born as a mostly normal girl.
One Piece: Whitebeard's relatively normal name is Edward Newgate.
Claymore: Most of the Claymores have quite plain names by occidental standards; examples include Clare, Teresa, Priscilla, and Helen.
X-Men gives us Jean Grey. She's had a number of names over the years (Such as Marvel Girl and Phoenix), but nothing ever really stuck. Across various media and incarnations, Jean is just... Jean. Lampshaded in one issue:
Cyclops: "Everyone, Jean and I have an announcement to make..."
Jubilee (off-panel): "Don't tell me, she finally got herself a real code-name?"
Jean: (Rolling her eyes) "Nothing quite THAT exciting, I'm afraid!" (For the record, they were getting engaged)
We also got Jubilee sarcastically referring to Jean as "Miss 'I'm too sexy for a codename, too sexy for a codename.'" Another time, in an X-Men: Evolution-based comic, Nightcrawler asked why Rogue was just Rogue, in superhero and in civilian life. Cyclops said "The same reason Jean's just Jean." When Nightcrawler asks about that, they're interrupted before any answer can be given.
All this becomes slightly hypocritical when you consider that Jubilee's "codename" is actually just her childhood nickname. But then, when your parents named you "Jubilation", what can you do?
And Rogue's real name - at least what we know of it - is Anna Marie.
A Norse god-powered alien cyborg named "Beta Ray" Bill. Just Bill, for short.
Also done with the aliens. Many of the aliens the agents encounter in the field have plain sounding names like Frank or Bob. This even includes a gigantic, subway-dwelling, omnivorous worm called Jeff. Presumably these are all assumed names, and they would make sense for those aliens living as humans. No explanation for the giant worm, though.
Clark Kent in Smallville. Sure, his birth name was Kal-El but it's very rare for anyone to call him that, and they never call himSuperman until the very last episode. Dude can bench press a glacier. His name is totally ordinary.
Early in Stargate Atlantis, Sheppard and a team capture a Wraith, which he names Steve. He keeps up the practice and later the Atlantis residents make an enemy of a particularly nasty Wraith named Michael and sometimes find themselves in Enemy Mine situations with another named Todd.
Somewhat justified in Farscape since aliens are expected to have stranger names than humans. Still, The Powers That Be were presumably invoking this trope when they decided to name the main character "John".
A trademark of sorts with many of Stephen King's books. All sorts of unique and fantastical characters and nary a "Jack Stone" or "Jack Steele" or any other "'John' Derivative + Hard Object" name to be found. Even the demonic antagonist of The Stand is named the very ordinary-sounding Randall Flagg. That's right; the Antichrist Expy is named Randy.
The Ender sequels feature a one-of-a-kind life form, an artificial intelligence with a soul. The ansible network and all computers linked to it function as her nervous system. She thinks at thousands of times the rate of human thought. The name she gave herself: Jane.
James Bond: Ian Fleming chose the name of his hero (named after an ornithologist) because it sounded so unexciting, although since then he's given the name an allure of its own. It also contrasts with the often outlandish names of the villains and peripheral characters.
Anne of Green Gables: Anne Shirley constantly laments having such a plain name. She wishes to be called "Cordelia", which she believes sound much more interesting. Though, if she must be called Anne, she's sure to remind you that it's spelled with an E, because without it, it looks even more plain and dreadful.
Harry Potter. In fact, Harry is one of the very few characters in his series to have a completely ordinary name. (Most of the characters with normal first names have weird last names.)
There are a lot of women named Mary in the Bible, in addition to the Mother of Jesus. Of course, now, variations of the name Mary are even more common throughout Christian and Islamic worlds.
In Dota 2, the true name of the Invoker, a mage who has lived centuries and has mastered the use of powerful invocations is simply Carl.
Subverted in The Curse Of Monkey Island. Guybrush asks one pirate his name, to which he is told "Bill". When Guybrush comments that this doesn't sound very piratey, Bill interjects with, "Cutthroat Bill".
In The Lord of the Rings Online you frequently run into a strange old lady called Sara Oakheart, who seems to know more than she is letting on. It's the perfect disguise, as her real name is Amarthiel, the Daughter of Doom, one of Saurons chief generals and a two thousand year old undead spirit, who had been spying on you the whole time.
While Solid Snake from Metal Gear Solid certainly has a cool-sounding code name; his real name is just "David".
Big Boss/Naked Snake's and Ocelot's real names, revealed during Metal Gear Solid 3: Snake Eater, are also rather plain: John and Adam — or rather, Ocelot's real name is "Adamska", a Hollywood-Russian form of "Adam" (it makes certain sense, since Ocelot is Russian-born and the game is essentially a Cold War spy film parody that takes everything it does seriously). In fact, Ocelot asks Naked Snake what his name is and then gives his own; when the latter answers simply, "John," Ocelot replies, "Plain name, but I won't forget it."
Pokémon Ruby and Sapphire gives us Maxie and Archie, the Magma and Aqua leaders. Unlike most characters, they have no theme nor pun to their names and seem to have been chosen because they start with the same letters as their teams and Japanese names, and sound a little bit alike.
Inverted in Thief with Viktoria, who has a suprisingly fancy and aristocratic name for a wood nymph.