Nostalgic Music Box

"The music box is broken, or is it? It starts to play, and a haunting tune fills the air..."

- Spike Spiegel, Cowboy Bebop

Specifically using music for nostalgic reminisces or flashback scenes, in the form of a music box. There's usually a fair amount of pining for lost innocence and/or love.

The opposite of Ominous Music Box Tune when the tune sounds much more sinister...

Anime

 * Lost Universe tends to feature a musicbox whenever the main character talks or thinks about his past.
 * Cowboy Bebop has two. The first episode, "Asteroid Blues", opens with a music box track titled Memory. The two-part episode "Jupiter Jazz" features a music box as a plot point. The track used for the melody is Space Lion (organ version).
 * Vision of Escaflowne has a nostalgic music box, but no flashbacks to go with it.
 * Elfen Lied, with the show's opening song. Among other things, Nyu can become Lucy when hearing it.
 * Sailor Moon, has a musical locket in the first season called the Orgel. This was inspired by a similarly shaped watch from the manga.
 * Noir has a watch with a music box inside of it as a major plot point. The box's song often plays over a flashback that has more and more revealed as the series goes on.
 * Aaeru in Simoun has a wind-powered music box given to her by her grandfather. The music it plays is actually a flashback on a cultural scale, though, as "The Door To A New World" is a song passed down from the earliest generations of Simoun sibyllae.
 * Nadja Applefield from Ashita no Nadja has one of these among her Memento Mac Guffins.  It later becomes very important,
 * A recurring song during the Arabasta arc in One Piece was a music box theme that played during Vivi's flashbacks.
 * There's one of these in Pandora Hearts that crops up so often that it's pretty much the musical equivalent of Arc Words.
 * Code Geass has "If I Were a Bird", which plays whenever Rolo's locket opens, as a symbol of his happy times with Lelouch. It also plays in full force
 * This is featured in Axis Powers Hetalia. Russia's character song starts out with a slightly eerie music box melody.
 * When alone, Suitengu of Speed Grapher obsessively plays a music box with a melancholic tune and thinks about his past. This ultimately leads to a flashback indicating this is the only possession left from his happy childhood, which was destroyed by loan sharks. Making things interesting, Saiga, the hero, independently whistles the same tune, foreshadowing the fact there's a connection between himself and Suitengu.
 * In Full Moon o Sagashite, Mitsuki learns of a song her father's band once performed called "Eternal Snow" . When she learns more about her mom and dad, among other things she finds a music box that plays the song's melody. From this point, the music box is played in almost every episode.

Film

 * Anastasia
 * For a Few Dollars More used two pocket watches, one belonging to Mortimer and the other carried by Indio, that played the same haunting melody, which was incorporated masterfully into the Morricone score. As it turns out, Indio's watch once belonged to Mortimer's sister, whom Mortimer seeks to avenge.
 * Pirates of the Caribbean has Davy Jones and Tia Dalma's music box lockets, which is the only thing shown to be able to drive the love-hardened vindictive sadist to tears.
 * Batman and Robin. Mister Freeze has turned an alarm clock, a glass jar, and an ice sculpture of his wife into an impromptu music box. He stares intently at it turn, but can only manage a single tear (that quickly freezes and sublimates given his icy demeanor).
 * To Kill a Mockingbird has a music-box-like theme at the beginning. The composer said he wanted the music to sound very pure and innocent.
 * The Blue Lagoon - film version, has a music box that plays Chopin's Nocturne Op. 9, #2 in E flat major. Emmeline says "That's Chopin! I can play it on the piano." It's used by the kids growing up as a connection with/nostalgic reminder of their life before the island. Sometimes they dance to it. None of this is in the book.

Live Action TV

 * Josette's music box in Dark Shadows.
 * On Lost, Rousseau has a broken music box that Sayid fixes for her. It reminds her of her husband and lost child after she's been alone on the island for sixteen years.

Music

 * The song "The Music Box Blues" by Tran-Siberian Orchestra, quoted at the top of the page
 * Ayumi Hamasaki's song "HANABI" opens with a music box, which continues to play as the song goes on. The song lyrics speak about a loved one who has died.
 * Emilie Autumn's "Gothic Lolita" opens with a music box that grows more and more distorted until the true song begins. The song's theme is lost innocence, so the music box sets a spooky tone that fits with the rest of the song.
 * Britney Spears has two songs using this sound affect: "Everytime" and "Baby Boy"
 * Abney Park's "The Secret Life of Dr. Calgori" starts off this way, shortly to be joined by steam valves and clockwork-like rhythmic percussion. Appropriate for the story of a 1800's era Mad Scientist slowly losing his memory.
 * "Herr Drosselmeyer's Doll" is much the same, but with less nostalgia and more... allure.
 * Siouxsie and the Banshees' 'Mother' on their 1979 'Join Hands' album. The eerily decelerating music box plays 'Oh Mein Papa' whilst the dual lyric details a love/hate relationship with the narrator's mother.
 * Surprised the opening of Voltaire's "The Man Upstairs isn't here, always get it, and the above mentioned "Gothic Lolita confused slightly.
 * The Rammstein song "Spieluhr" involves one.
 * Japanese singer/cellist Kanon Wakeshima has one in the instrumentals "Sweet Dreams" and "Shakespeare No Wasuremono ~Epilogue~", as well as in the beginning of the single "Lolitawork Libretto ~Storytelling by Solita~".

Theater

 * The monkey music box in The Phantom of the Opera.

Video Games

 * Yasunori Mitsuda loves this trope, as the nostalgic themes in his best-known games all have music-box versions of the main theme. In fact the music box themes almost all have the same track name: Kokkoro (Heart or Soul).
 * Chrono Trigger's nostalgic theme is eventually expanded upon in at least one of the endings, in a song called "To Good Friends" - it starts off identically, but eventually segues into a fully-orchestrated arrangement of the same theme, and it is beautiful.
 * Radical Dreamers and Chrono Cross
 * Xenogears
 * Bonus points for actually appearing in the game.
 * Disgaea's main theme is music box playing.
 * Final Fantasy VIII - The Laguna flashbacks involving Ellone and her daughter.
 * Final Fantasy V does a similar thing with Bartz's music box in his old home in Lix. Never mind that he's listening to it and recalling while a squatter bard sits there impassively . . . it's still a pleasant tune.
 * Final Fantasy IX has a phonograph music box at the Inn in the Black Mage Village. If you have certain special items purchased at the auction house in Treno, it will play pieces from earlier Final Fantasy titles corresponding to the special items.
 * Pokémon Mystery Dungeon: Explorers of Time/Darkness/Sky has a nostalgic theme played on a music box that plays in scenes where you and your partner are feeling especially tender, as well as when you're about to go to bed for the night.
 * Earthbound - The final rendition of the Eight Melodies, just before.
 * In the prequel, you learn the first part of the game's version of the Eight Melodies from a music box that was in the possessed doll you just fought. Also, the ending tune starts and ends with a music box rendition of the Eight Melodies.
 * Silent Hill 2.
 * Fable 2 starts with you in your childhood, trying to buy a magical music box. The music box's theme sometimes appears in the game's score, particularly during flashbacks and dreams of your childhood.
 * Super Mario World 2: Yoshi's Island has an opening theme that sounds as though it is being played on a music box (it even slows down at one point, and has to be rewound). This theme reappears in Yoshi's Island DS, and is the best song on the soundtrack, despite being played in a different key.
 * Paper Mario features this in both The Thousand-Year Door and Super Paper Mario with specifically designated "Memory" themes that used a music-box-like effect when a particularly Tear-Jerking moment was happening.
 * Speaking of Mario, the Lumas' theme from Galaxy. Bonus points for being played 
 * On the "The End" screen of Baten Kaitos, a music box rendition of the game's main theme plays.
 * Same with Super Mario RPG.
 * There's a music box in Quest for Glory IV belonging to the old man, Nikolai, who is searching for his wife. If you turn on the music box while in Nikolai's house, the old man will wake up and ask for Anna, thinking that she has come home.
 * The title screen of Xenosaga Episode III plays a nostalgic music box version of its Award Bait Song, "Maybe Tomorrow."
 * In Tactics Ogre: Let Us Cling Together, Lars carries his late wife's music box as a memento. The track played is titled Box of Sentiment. The melody is later orchestrated in Emotion and Absence of Mind.
 * The final results screen after the credits of Devil May Cry has one of these playing, and it's very pretty.
 * In Professor Layton and the Diabolical Box, one of these plays during The Reveal. In this case, the music isn't the symbolic part, it's The music box track, Iris, is used a few minutes later in orchestrated form for the end credits. And it's one hell of a Tearjerker.
 * Sad and sentimental scenes with Ilya in Fate/stay night (including in UBW) uses a music-box version of "Die Lorelei", a German folk song, as background music. It's used to underline Ilya in her innocent and humanizing moments, which becomes a source of Lyrical Dissonance since the original song is about a siren who uses her beautiful song to drown sailors.
 * Game Over screen in Blaz Blue has a short sad music box music. Later (especially in Continuum Shift) promoted to flashback music. Also turns out to be theme song of an important unplayable  character with even more symbolism. Also has a vocal version in one of the albums but not in the games.
 * A music box version of The Shadowlord's theme plays in Nie R when The Shadowlord is on his final bit of health. It's meant to represent how at this point he just wants to die.
 * The Muv-Luv series of visual novels has A World To Protect, a rearrangement of the main theme. It first plays in Unlimited when, it then plays in Alternative when
 * Symphonic Rain has several music box versions of the opening and ending theme playing during especially poignant moments.
 * All is Shut Down #1(bad ending) from Ray Crisis.