The game also uses the ice world theme from Super Mario Bros. 3 when you receive a message from a mysterious informant, "Mr. X".
Anything in the Paper Mario/Mario & Luigi series that would logically play music WILL play something from Mario's old days. Case in point: the record player in Boo's Mansion from the first Paper Mario, dust and all.
And some things that wouldn't logically play music; there's a vase that's also in Boo's Mansion that, if Mario jumps into it, makes him into an 8-bit Small Mario while the Super Mario Bros. theme plays.
Leaving the new chapter screen on long enough will also cause it to start playing
And Mario will whistle his original theme music in Super Mario RPG when he hops in the shower at the inn in Marrymore.
Also in Super Mario RPG: "Long, Long, Ago." You went behind a curtain in Booster Tower and "Super Mario Bros." theme fromm 1-1 started playing. Mario also turned back into his 8 bit sprite.
In Trapt, the first "Dark Illusion" (a kind of particularly gory and lethal traps inset in the enviroment) that the player is likely to find, is "The Man-Eating Music-Box" — which plays the game's "Melancholy Theme" as it crushes the helpless victim within its gears...
Wesley Stickler's cell phone ringtone in Apollo Justice: Ace Attorney is one of Klavier Gavin's band's songs, Guilty Love, sped up to almost double the tempo.
Klavier himself plays a recording of Guilty Love by way of an introduction in court. It's somewhat safe to assume that every single repeat of the theme tune afterwards is just Klavier toeing "play" on the CD player beneath his bench.
Even Phoenix's cell phone is like this: his plays the Steel Samurai theme song.
In case 1-5, Ema Skye's cell phone plays the Steel Samurai theme song as well. This allows Phoenix to pass it going off in the parking garage as his when the detective at the scene asks what just happened. Or, possibly, he set it to the Steel Samurai theme tune because of this incident (in cases 1-1 to 1-4, his cell phone had a generic ringtone).
Duke Nukem 3D has several references to the main theme, "Grab Bag" — Duke whistles it during the end of the second episode, and it also reappears in muzak form in the Atomic Edition level "Shop & Bag".
Inverted in Final Fantasy VI; the first time in the game that Celes's theme is heard (indeed, hers is the only one that doesn't play during the rename screen) is when Celes sings it in an opera.
In Final Fantasy VIII, the game's end theme, "Eyes On Me," is a hit pop song in-game and is first heard as an instrumental piano piece played at a nightclub by Julia Heartilly, who is soon inspired to write lyrics for it thanks to Laguna's influence.]
The game's end theme in Final Fantasy IX, "Melodies of Life," is also important in-game. Zidane first hears Garnet/Dagger singing it on "la" in Dali and later in Lindblum. He asks her what it is and she admits that she doesn't know, and can't even remember where she learned it, but singing it comforts her when she feels sad or lonely. Zidane says that it must be a mystical song. He later hears her singing it in Dali and when she stops, he tells her that it's okay for her to kee singing "'Cause it's our song, right?" As they float out to sea on a boat, they hear the song coming from the Eidolon Wall and hearing it causes Garnet/Dagger to have a flashback and remember some of the details of her early childhood. Finally, at the end of the game, everyone believes Zidane to be dead, but he comes back. Garnet/Dagger asks him how he survives and he explains "I didn't have a choice. I had to live. I wanted to come home to you. So... I sang your song. Our song." The game ends and the full vocal version of the song plays during the credits.
Zelda plays the game's theme, the Ballad of the Goddess, on her harp. The Ballad itself is an inverted cameo of Zelda's Lullaby from Ocarina of Time - this is Foreshadowing, as Zelda is the Goddess, reincarnated.
This also serves as a Call Back, since one episode (season 5's "Lisa vs Malibu Stacy") ends with Homer doing pretty much the exact same thing.
At the end of her concert in Mega Man Star Force 3, Sonia Strumm performs a new song she's composed called "Shooting Star," which happens to be the game's opening theme.
In one of the Hot Springs events of Tales of Symphonia, the female characters are singing the game's opening, "Starry Heavens". It's of course Lost in Translation in the US and European versions as the opening J-pop song is replaced by an original instrumental work.
In the third Monkey Island game, you can talk to Edward van Helgen about a horrific sea voyage where he and his crew were haunted by a diabolical, cacophonous melody coming from the wreck of a ship they had visited. Most of his crew went mad and threw themselves into the sea. When Guybrush asks him how the tune went, van Helgen will hum the classic theme to the Monkey Island series.
Mega Man 7 contains an example — in the introductory cutscene, Mega Man is helmetless and is riding in a truck to the intro stage. When he puts on the Metool helmet, a short theme with an abrupt, dissonant Record Needle Scratch-esque ending plays. Mega Man then dons his iconic blue helmet, and the recurring "Robot Master Selected" theme plays.
In Fallout 2, a mentally-retarded janitor can be found singing (with a considerable stutter) the song Maybe, the theme from the first game. It's a place to boost your Karma Meter by either praising him for it, or telling him to shut up.
While a bit of an Easter Egg, each of the buttons on the main screen in the Peggle series makes a little "bloop" noise when the mouse rolls over it. These aren't random; playing the closest thing to a theme that Peggle has (Ode To Joy) produces a little congratulations scene.
Pokémon Gold and Silver have Team Rocket hijack the radio tower as part of their plan to find their missing boss, Giovanni. The music that plays on all radio broadcasts while they do this is the same theme that plays when a Rocket Grunt challenges you to a battle.
The alien shopkeeper who sells you weapons in Xenon 2 Megablast is listening to a tinny version of the game's theme tune when he appears, then turns it off to do business.
In the elevators in Mass Effect 1, one of the tunes piped in is a muzak version of the game's main theme.
In an old DOS game called Normality, the opening cutscene shows the protagonist being arrested for whistling. The tune he was whistling was the game's theme tune.
Partial example: The Mega Man X series uses a rocking metal cameo of the musical stinger that plays when you pick a robot master in the first Mega Man game.
At least one song in every Silent Hill game after the first includes a part of the track playing notes from the original game's theme. Namely Theme of Laura, Hometown, One More Soul to the Call, and Hell Frozen Rain.
The Pikmin will hum the first few bars of their theme tune when traveling.
An Easter Egg sees the Pikmin hum the song used in Japanese advertising for the game, "Ai no Uta," in-game.
Quintessence: The Blighted Venom: The opening song (To Realize) is not only played in-character, but exists in universe before hand, and has some plot significance. (Not much, though some.) And played by the main characters; one using an ocarina (Reivier) and one using a piano. (Lunair) Sadly not at the same time.
Super Robot Wars Alpha 3 has Macross 7's Basara write a song that he wanted to record with Lynn Minmei; it doesn't actually get played until the final battle, where it inspires the heroes to say "Screw Destiny" and fight the insanely powerful Final Boss. The song is, of course, the theme song for Alpha 3 itself. Bonus points since Yoshiki Fukuyama of JAM Project (the band who originally did the song) provides Basara's singing voice.
In Lunar: The Silver Star, Lemia's regimental band, if given the opportunity to play, will perform the game's opening theme.
The menu theme of the Kingdom Hearts series, "Dearly Beloved," appears as a solution in Kingdom Hearts 3D. Two Sound Ideas are needed, the melody and the chords, and the resulting harmony seals a dark magic away. Also an example of Title Theme Drop, since it is the only music playing during those cutscenes.