My Immortal. The many spellings of Ebony's name: Enoby, Evony, TaEbory, Tata, Tara...
StarKitsProphcy features a wide variety of misspellings of character names. At times, it's hard to tell what the correct spelling of a character's name is supposed to be. As such, it's impossible to tell if the character "Soul", who shows up in the last chapter for no apparent reason, is supposed to be Sol or not.
Pokéumans: Larry the Loudred MC has a variety of spellings used for his surname—examples include Bellowitch, Belowich and Bellowich. No-one's entirely sure what's correct, but the pun is apparent.
The Slender Man Mythos fic By the Fire's Light pays tribute to the many variations on Slender Man's name, including Slender Man, Slenderman, and slenderman at different points in the story coming from different characters.
From Kill la Kill AU, we get Rei's last name Hōōmaru, which, alternatively is spelled "Hououmaru". Apparently, her last name is hard spell and is often misspelled as "Houmaru". In terms of alternative spellings, we get Ragyo's name being spelled as "Ragyou" and Ryuuko's name being spelled as "Ryuko" and her nickname Riley, being spelled as "Rylie".
Played with with Undermon, where Toriel is actually spelt Torial. Which, considering the Aura which she has due to the history of the fic, hints at which Legendary she has the Aura of.
In Children of an Elder God, the authors often misspelled Asuka's surname, writing “Langely” instead of “Langley”. It's lampshaded in chapter 21: Shinji's spiders spun a heart-shaped web with Asuka's name written on it. Asuka says it's very sweet... but her name is misspelled.
"Except it's 'Langley' not 'Langely', Shinji-kun," Asuka said, pointing.
Discussed in the My Little Pony: Friendship Is Magic fanfic On The Importance Of Spelling. Shining learns that he's been spelling his wife's name incorrectly as "Cadence". Cadance notes that since "Cadance" is a diminutive form of her 'real name' that the spelling isn't really that important. The two then get into a discussion on the different ways to spell Cadance's name. As it turns out, Shining Armor's legal name is "Shining Armour" but he doesn't use the "u".
The Twilight Man: Caesar Zeppeli's name is spelled Cesare when he debuts in chapter 6 of the interquel Let the Good Times Roll. The author confirms that he will change it to his canon spelling by the events of Part 2.
Parodies
Parodied in Those Lacking Spines, where when facing down a rabid group of Fangirls the main characters invoke this trope by getting them to fight over the spelling of Final Fantasy VII character names, ranging from the classic Aeris/Aerith to eventually Gratuitous Japanese like Vincent/Binsento.
Parodied in The Labyrinth Fanfic Academy when writers of bad Labyrinth fanfiction are forcibly restrained by sets of Helping Hands nicknamed "Saraï (Sarah), "Jereth" (Jareth), "Pluto" (Ludo), and "Hoggel" (Hoggle).
Pariodied with poor G-Boy, Katarina's fiance, in Katarina Claes At Hogwarts, as thanks to a ritual by his mother his name is frequently changing.
. Shining learns that he's been spelling his wife's name incorrectly as "Cadence". Cadance notes that since "Cadance" is a diminutive form of her 'real name' that the spelling isn't really that important. The two then get into a discussion on the different ways to spell Cadance's name. As it turns out, Shining Armor's legal name is "Shining Armour" but he doesn't use the "u".