The main character of Savatage's Streets: A Rock Opera is known only by his drug dealer nickname "DT Jesus". The "DT" stands for both "de-tox" and "downtown". The All There in the Manual story provides another nickname unused in the lyrics, "the Savior on Avenue D".
The protagonist of Melanie Martinez's Concept Album, "Cry Baby", is only ever referred to as that. According to the song "Cry Baby" she received the nickname because she cried a lot as a child. The music video however implies that is literally her name, as her older brother wrote that on her birth certificate (though it's possible they changed it later).
There's that one traditional African song made famous thanks to Miriam Makeba's rendition that most people refer to as "The Click Song"... At least this example is justified, as they are usually unable to pronounce the actual title due to click consonants present both in the title ("Qongqothwane", the Qs being said click consonants) and in the song itself.
Musicians
Rappers too numerous to mention.
Hiram Williams was known to the world as Hank Williams.note His son Hank Jr. and grandson Hank III are actually examples of Middle Name Basis—they're respectively Randall Hank and Shelton Hank Williams.
Ace Frehley, formerly of KISS. Only his wife addresses him by his real first name, Paul.
The bass player, Fieldy. Most people don't know his real name is Reginald Arvizu.
To a lesser extent, Korn's guitarists James "Munky" Shaffer and Brian "Head" Welch.
Evelyn Evelyn is a performance art duo supposedly made up of Conjoined Twins, both named Evelyn. Their official names are Eva and Lynn Neville, but during their Hilariously Abusive Childhood nobody ever bothered to remember which one was which, so the twins themselves can't remember either.
Canadian Synth Rock band The Birthday Massacre have stage nicknames; while some members just use their real names (Owen, formerly O-en Falcore and Nate) some band members' real names are not public knowledge (Rainbow and Chibi, as well as former members Aslan and Dank).
When asked about his name in an interview, keyboardist Christian Lorenz responded that his nickname Flake is his proper name.
Rhythm guitarist Paul Landers was born Heiko Hiersche, which he hated, so he started going by his second name, Paul (and then took his first wife's surname). Only his father always continued to call him Heiko.
Angel guitarist (and the inspiration for Frank Zappa's song, "Punky's Whips") Punky Meadows. Sounds a lot better than his real first name of Edwin.
Johnny "Guitar" Watson: The word "Johnny" and the word "guitar" in his name, derived from the film Johnny Guitar, are practically the official way of referring to him in the press.
1920s blues singer Robert Hicks also worked as a cook at a Georgia barbecue restaurant, so his record label combined this with Everyone Calls Him "Barkeep" and billed him as Barbecue Bob.
Tré Cool (Frank Edwin Wright III) and Mike Dirnt (Michael Pritchard) of Green Day. Averted by Billie Joe Armstrong, whose name really is Billie Joe.
Many Black Metal artists' pseudonyms become more well-known than their real names: More people are probably familiar with original Mayhem guitarist's pseudonym "Euronymous" than his real name, Oystein Aarseth.
Ringo Starr: Richard Starkey is the only Beatle not known under his real name. James Paul McCartney used his middle name "Paul" to distinguish himself from his father.
Ozzy Osbourne, Tony Iommi and Geezer Butler of Black Sabbath; their real first names are John, Frank and Terence, respectively. Ozzy's nickname is so well-known that he now prefers to go by that name; only his siblings and his ex-wife Thelma refer to him as John.
Zakk Wylde of Black Label Society his real name is Jeffrey Phillip Wielandt.
Pantera Abbott Brothers Dimebag Darrell and Vinnie Paul. Their real name is Darrell Lance Abbott and Vincent Paul Abbott.
(James) Shannon Larkin, the drummer from Godsmack, goes by his middle name.
Mastodon lead guitar/vocalist Brent Hinds, his first real name is William.
tool vocalist Maynard James Keenan, his real name is James Herbert Keenan.
Machine Head vocalist Robb Flynn was born as Laurence Matthew Cardin and guitarist Wacław "Vogg" Kiełtyka.
Averted with Eminem, as he is also known by his alter-ego Slim Shady, and his real name Marshall Mathers.
Madness' albums usually list their lead singer under his real name Graham McPherson, but nobody actually calls him that - everybody calls him Suggs. The same applies to his former bandmate Cathal Smyth, known to the world as Chas Smash.
Creed: Vocalist Scott Stapp was born as Anthony Scott Flippen but he used his stepfather's surname. Drummer (Thomas) Scott Phillips goes by his middle name.
BluesSinger-Songwriter Keb' Mo' is an unusual variation, since his Stage Name is just a downhome version of his actual name, Kevin Moore, and in fact, he went by Kevin Moore earlier in his career.
Melvins frontman Buzz Osborne, a.k.a. King Buzzo, is almost never referred to by his given name, Roger.
R3hab never gets refered to as his real first name, "Fadil". Not even once.
Avenged Sevenfold: Most of the band members used stage name, M.Shadows (Matthew Charles Sanders), Synyster Gates (Bryan Elwin Hanner Jr), Zacky Vengeance (Zachary James Baker), Johnny Christ (Jonathan Lewis Stewart) and late The Rev (James Owen Sullivan).
Zig-zagged in the case of Frank Black, formerly Black Francis, solo artist and Pixies frontman, whose real name is Charles Thompson. He's always been known professionally by one of those two stage names, but his bandmates publicly refer to him as Charles.
made famous thanks to Miriam Makeba's rendition that most people refer to as "The Click Song"... At least this example is justified, as they are usually unable to pronounce the actual title due to click consonants