Bootstrapped Leitmotif

A slightly more specific version of Bootstrapped Theme. The latter refers to a repeated theme that was initially meant to represent a character, place, mood, or other specific part of the story but eventually came to stand for the series as a whole. A Bootstrapped Leitmotif on the other hand, is where a repeated theme that is initially tied to something else within the narrative mutates into a specific character's Leitmotif.

This is often because the song in question is played during scenes that focus heavily on a specific character. In video games, this commonly occurs with background music for stages or levels strongly associated with a certain character, or the character's Boss Battle music. Sometimes a character may already have a Leitmotif, but a different song that is more readily identified by the audience usurps it and becomes more widely accepted and recognized.

Anime and Manga

 * Dragonball Z applies for the original and English versions:
 * Original version: Majin Buu's theme. It's actually the Super Saiyan theme variation for the Majin Buu saga (both the Freezer and Cell sagas have each its own variation of the theme), but it appears so many times during the Majin Buu saga as a Battle Theme Music that it ended up associated with him instead of with the good guys. It's difficult to find anyone who doesn't think of Majin Buu when hearing it.
 * To a lesser extent, Freezer and Cell's themes also apply. These are better in the sense that, at least, they're exclusive to that saga, but still fit here because they're not exclusive to Freezer and Cell respectively.
 * The Saiyans' theme ended up being Vegeta's theme, because he's by far the most important of the (evil) Saiyans, and the only one who survives. Although it appears whenever one of the evil Saiyans is on screen (it first appears with Raditz), after Raditz and Nappa die it can only appear with Vegeta on screen. It doesn't help that it's used much after than even the Namek saga (this tropes remembers hearing it during at least during the Androids saga, when Vegeta appears to save Goku from Android 19).
 * Pretty much all the Dragonball Z characters leitmotifs (except Gohan and Piccolo, who have an official leitmotif) fall into this trope. Broly and Cooler also have an unofficial leitmotif.
 * English dub: Gohan's Super Saiyan theme. It's actually the Hyperbolic Time Chamber theme, as the first comment says, but everyone knows it either as "Gohan's Super Saiyan theme" or "Gohan's Super Saiyan 2 theme", because of the 5 seconds or so that can be heard when Gohan transforms to SSJ2 for the first time. It doesn't help the fact that Gohan doesn't have an official Super Saiyan theme.
 * Franky in One Piece got this with the third part of a soundtrack tune called "Serious Games." The only other previous use in the series had been for one of Usopp's Crowning Moments of Awesome. It is now heard regularly when Franky does anything and on his eyecatches.
 * Susumu Hirasawa's "Forces," due both to its use during Guts' first battle with the Hawks and its use in the "next episode" trailers, has come to be considered the main theme of Berserk.

Film

 * Godzilla has two main themes: the slow, dark "horror" theme from the original movie when he rampages through Tokyo, and also from the original movie, the up-tempo Self Defense Forces march, which become so associated with the monster that even the composer began calling it Godzilla's Theme. Nowadays, both are used relatively equally, depending on what kind of mood is being called for.
 * "Hooray For Captain Spaulding" from Animal Crackers became Groucho Marx's theme song in this manner.
 * Most explicitly as the theme to You Bet Your Life.

Live Action TV

 * On Arrested Development, the "Oscar is Buster's real father" theme became the general theme for Oscar and I'm Oscar Dot Com.

Professional Wrestling

 * Linda McMahon's entrance theme began life as the theme for WrestleManias X to XIV.
 * On a related note, Vince McMahon's theme, "No Chance in Hell", originally began as the theme to the 1999 Royal Rumble.

Video Games

 * Arguably the most famous case in the medium is Link. Link was never given a Leitmotif in the first games, despite almost every other character getting one. However, ever since The Legend of Zelda the Wind Waker, the original game's title/overworld theme appears to have become Link's motif as well, being a case of BOTH a Bootstrapped Theme (as the Main Theme of the series) AND a Bootstrapped Leitmotif.
 * It shows up again as the, practically canon-izing its status as this trope.
 * The stage music themes in Street Fighter II. They ended up being the themes of the characters who uses it as their home stage.
 * Funny that Fox McCloud never got his own theme, yet his rival Wolf has a personal theme. It is usually attributed to Fox that Area 6 in Star Fox 64 is his theme, as it was used in Super Smash Bros. Brawl and Star Fox Command.
 * The original Star Fox Corneria theme is also very popular, though it took Super Smash Bros three games to finally implement the theme into Brawl's soundtrack.
 * A slowed down version of the Pollyanna theme was used as Ness' house music in Earthbound. Not entirely recognizable at first, though. While not his official leitmotif, it's frequently associated with him.
 * In Final Fantasy VII "Those Chosen By the Planet" is Sephiroth's Leitmotif. However, his battle tune, "One Winged Angel", has mutated into his tune in the minds of the fandom and, as a consequence, in the compilation.
 * "One-Winged Angel" does incorporate "Those Chosen By the Planet" though, so it's not so much a completely different Leitmotif as it is a Boss Remix that became more popular than the original song it remixed.
 * Also, Cloud was never attributed a specific theme, so he appropriated the game's Overworld theme and Main Theme as his own. It roughly follows his character growth throughout the game, variations of it are used during moments of powerful emotion for Cloud, and it coincidentally disappears from the Overworld at the same time Cloud leaves the party, to be replaced with the Meteor theme. It's no coincidence that it plays again in the Compilation over the credits of Crisis Core, to indicate that Zack's torch has been passed to Cloud.
 * Final Fantasy IX: Melodies of Life (at least the instrumental version) was largely Garnet's theme, as she hums it throughout the game. But ask anyone what song they associate with the game, it's pretty much just that.
 * Fire Emblem Tellius got the theme "Eternal Bond" as the Greil Mercenaries' charging theme, but in Super Smash Bros Brawl it was renamed "Ike's Theme", and now is remembered as such. To be fair, Fire Emblem Tellius did use it in a character Leitmotif fashion in several scenes.
 * The song called "Theme of Samus Aran: Galactic Warrior" in Super Metroid originally, is now probably better known as the music for Upper Crateria. Instead, the main theme of Super Metroid itself has since mutated into Samus' own character theme. This video gives a good background on the history of the song.
 * Super Metroid used three different songs for its various boss fights. The one that played during both escape sequences, as well as the fights with Ridley, Draygon, and the Torizo, has come to be almost exclusively associated with Ridley and has been remixed for every appearance he has made in the series since. Even Brawl refers to it as "Vs. Ridley" (the name of the track in Metroid Prime, BTW).
 * The composers of the Halo soundtracks said that they didn't intend to apply leitmotifs, but many music pieces can be bootstrapped to characters or locations, eg "Enough Dead Heroes" = Cortana, "Shadows" and "Devils...Monsters" = the Flood, "The Last Spartan" = Master Chief, "Weight of Failure" = the Arbiter (and later the Separatists), "Destroyer's Invocation" = Tartarus, "High Charity" = the Prophets, "Penance" = Delta Halo, "Earth City" = the Scarab, "Under Cover of Night" = Sgt. Johnson(his death scene uses a Dark Reprise of it), "In Amber Clad" = Cmdr. Keyes, "Farthest Outpost" = the Ark.
 * "Orbital Drop Shock Trooper" = the ODST team, "The Battle Begins" = Battle for Reach, "Noble Mission" = Noble Team, "Lone Wolf"/"Noble Six" = Noble Six, "Follow Our Brothers" = Elite Seperatists, "Ashes" = Kat/New Alexandria, "Make It Count" = Jorge, "Finish the Fight" = the Portal, "Sword Control" = Sword Base, "Rain"/"The Rookie" = The Rookie, etc.
 * Several songs in the Castlevania series have become recurring themes for the characters that starred in the games where they debuted. Rondo of Blood has "Bloodlines" (the first stage theme) and "Slash" (the theme of one of the alternate stages), which have become respectively associated with Richter and Maria. "An Empty Tome" from Order of Ecclesia, the song that plays when you first enter the castle, is repeatedly used as Shanoa's theme.
 * In the Ys series, "Theme of Adol" and its variations is implied to be the titular hero's leitmotif, although it never seems to be directly connected with him in-game.
 * The second game in the Ace Attorney series, Justice For All, has a track called "Search - In the Midst 2002". While not technically considered a character theme, every instance of the song is connected to the defendant of the case it appears in, Matt Engarde, so is is any wonder that it is generally considered to be his theme?
 * Oddly enough, the same track ends up inverting this trope in the following game. While it was practically a Leitmotif in JFA, it becomes a general 'dark secret' theme in Trials and Tribulations.
 * In the same case, when Miles Edgeworth finally returns, the theme "The Great Revival" plays many of the times he is on screen, along with other non-Edgeworth-y events, such as . Jump ahead 7 years, and The Great Revival is remixed into numerous themes of Edgeworth's spinoff game, including the Objection theme and end credits, essentially cementing itself as Edgeworth's Leitmotif. It gets remixed again in the second Edgeworth game.
 * Another inversion of this trope occurs in the Fire Emblem Akaneia. In Shadow Dragon, the track entitled "The Proud Commanded" was the Leitmotif for Camus and Michalis. In New Mystery, it's used as background music for any vaguely-intimidating boss, and even a few recruitable characters!
 * Modern Warfare 2 has: "Contingency" = TF141, "Code of Conduct" = Shadow Company, "Siege"/"Infiltration" = Washington DC, and plenty of others.
 * Gears of War 2 has "March of the Locust" = Locust Horde, "Hope Runs Deep" = COG, "With Sympathy" = Maria, "Rolling Thunder" = Delta Squad(YMMV for this) and so on.
 * The Tomb Raider title theme and its variations = Lara's theme.
 * In the Touhou Project, a character's Leitmotif usually ends up being the music from their boss fight, but this trope happens a few times. Hong Meiling, Alice Margatroid and Youmu Konpaku all get their stage themes as Leitmotifs (along with their boss themes); Suika Ibuki gets her pre-battle theme (again, along with her boss theme). Also, midbosses (Daiyousei, Koakuma, Lily White etc.) usually don't have their own leitmotifs, so they tend to get associated with the theme of the stage they appear in.
 * In the Touhou Project, a character's Leitmotif usually ends up being the music from their boss fight, but this trope happens a few times. Hong Meiling, Alice Margatroid and Youmu Konpaku all get their stage themes as Leitmotifs (along with their boss themes); Suika Ibuki gets her pre-battle theme (again, along with her boss theme). Also, midbosses (Daiyousei, Koakuma, Lily White etc.) usually don't have their own leitmotifs, so they tend to get associated with the theme of the stage they appear in.

Webcomics

 * Happens all the time in Homestuck. This webomic has its own music team who typically compose themes based on their own visions, but which will often get used in the comic in a completely different context than they imagined. A specific example is "Crystamanthequins", a song originally supposed to be music for Dave. It was later used in this flash and became associated with Vriska and Terezi instead; lately it has been showing up as a Recurring Riff in that context.
 * One of John's themes, "Doctor" ended up becoming a theme for.

Western Animation

 * Sideshow Bob's theme. His theme is the title music for Cape Fear, since the episode it was first used in was a parody of Cape Fear. It wasn't meant to represent Bob, but since he was the bad guy, it naturally played only when he was onscreen. The producers ran with it and now it's quite explicitly his theme, always playing when he first appears in an episode (just in time for Bart and Lisa to shout in unison: "AAAAAAH! SIDESHOW BOB!").