Assassin's Creed II has Ezio's Family. First played over the opening credits, remixed several times as "Earth" which plays when Ezio recovers his father's Assassin robes and then as "Venice Rooftops", which plays during chases, races and courier missions (occasionally). Played in all it's glory over the credits of both II and Brotherhood. And don't lie. There were manly tears.
The Final Fantasy series is in love with this trope. Nobuo Uematsu, the composer of much of its music. is known for creating memorable leitmotifs for characters, locations, and events. In Final Fantasy VI, for example, almost all of the playable characters (and some of the villains) have their own leitmotif (with the exception of the twin brothers Edgar and Sabin/Mashe, who share one). Terra's leitmotif, which is also the Overworld Map theme, is effectively the Theme Tune for that entire game. Even more well-known, though, are the Recurring Riffs for concepts that span more than one game, such as the Crystal Theme/Prelude, the Final Fantasy Theme/Prologue, the (much-remixed) Chocobo Theme, the Moogle Theme, and the Victory Theme.
Terra's true character theme is actually called "Awakening". Celes's character theme is the famous opera song "Aria Di Mezzo Carattere" played slower and more sad in tone.
Dancing Mad, the music that plays during the party's final confrontation with Kefka Palazzo, incorporates numberous letmotifs that, when you sit down, listen to them, piece them together, and think about it sums up everything Kefka is so perfectly, it couldn't be the final boss music for anyone else but him.
The ending music for Final Fantasy VI is often cited as Uematsu's magnum opus, as it takes new versions of every character theme, plus the main Final Fantasy theme (a total of fourteen pieces) and blends them together into a single 20 minute piece. It's impressive enough to make you forget you're listening to video game music.
Likewise Yasunori Mitsuda, composer for some of Square's other games, including Xenogears. In a great case of combining forces, Mitsuda and Uematsu co-composed Chrono Trigger, which has some of the most memorable Leitmotifs.
In said game, "Lucca's Theme" probably got played the most, as it starts up whenever anything science/awesome/awesome science-related happens. In fact, the track name is simply "Fanfare", and is adapted, in two separate versions, as the victory theme in the sequel, Chrono Cross. This doesn't mean it isn't Lucca's theme, though - it plays when you talk to her in the End of Time, the same way everyone else's theme does.
"One-Winged Angel" does incorporate the tune of "Those Chosen By The Planet" in part though, but it can be a bit hard to pick out if you're not listening for it.
Crisis Core features no less than eight songs titled "Theme of Crisis Core (Subtitle). The theme also appears in songs that don't follow this naming convention, such as "Burden of Truth" and "The Burdened".
Dirge of Cerberus uses two different motives throughout, which can be considered "Vincent's Theme" and "Lucrecia's Theme".
Gilgamesh of Final Fantasy V, from his second appearance on, is one of only two enemies in the game to get his own theme, "Battle on The Big Bridge". This one was so memorable that when Gilgamesh made a cameo in Final Fantasy XII, his theme came with him (in a well-done orchestration, at that) as well as a big bridge to fight on.
On top of that, The fight against Necrophobe, when the boss just doesn't seem to die, then suddenly you hear the theme. Crowning Moment of Awesome for Gilgamesh.
Tidus's theme in Final Fantasy X is remixed into a more upbeat and generic Blitzball theme.
In Final Fantasy XII, the themes are actually remixes of each place special(s) to the characters. Example, Ashe's theme is really the theme song of the creepy dungeon Giruvegin, and the Pharos, because that's where her father placed the magicite. You can also hear the theme of the Tomb of Raithwall.
The leitmotif for Final Fantasy XIII is "Fabula Nova Crystallis". Tracks contain this melody include two location themes, three event themes and a character theme with lyrics to boot.
Lightning's Theme is also used for a Battle Theme, aptly named "Blinded by Light".
Final Fantasy Mystic Quest subtly pokes fun at the idea with the character of Tristam, whose leitmotif begins playing just before he appears on screen. The main character, Benjamin, apparently hears this music and begins looking around for him whenever it begins playing.
Final Fantasy IV was the first game in the series where many different characters are given leitmotifs. Nearly all of the protagonists have one, as do some of the villains, most notably Golbez, with "Clad in Black." Nothing says "Oh shit, I'm about to get my ass kicked by the Big Bad" quite like those Ominous Pipe Organs.
Don't forget the Theme of Love, Rosa and Cecil's relationship theme. The theme is so popular and well known in Japan, it's now being included in many schools music books over there.
House of the Dead 1 and 2 feature the Magician boss leitmotif. The series also has the recurring "Game Over" and "Chapter Clear" ditties.
Xenogears has leitmotifs for Bart (Bonds of Sea and Fire) and Chu-Chu (The Sky, the Clouds, and You) among others.
Kingdom Hearts also uses leitmotifs extensively, particularly in the sequels. Kairi has 4 different variations on her leitmotif, while Sora only has one. Bosses also have their own leitmotifs. If a character is fought as a boss at some point in the game, their battle music will be a remix of their theme. Nearly all of Organization XIII's battle themes use the piano. "The Other Promise" and "Rage Awakened" are also remixes of Roxas and Terra's themes, respectively.Ventus's theme as well as Vanitas's battle theme include strains of both Roxas and Sora's themes.
"Dearly Beloved" and "Destati" are essentially leitmotifs for the entire series.
Characters and concepts also have instruments and Recurring Riffs associated with them. Ominous Pipe Organs for the Heartless, mournful piano melodies for Nobodies, strings for Keyblade Wielders, chanting for the heart in general.
In the series, certain bosses' battle music will sound suspiciously familiar. Xion's boss music in Kingdom Hearts 358/2 by 2 Days has strands of Sora's. Kairi's, Naminé's and her own theme as well as Dearly Beloved.
The secret boss of Kingdom Hearts: Birth by Sleep (Mysterious Figure) has 3 other character's theme in his battle music: Terra's theme, Darkness of the Unknown (Xemnas), and Lord of the Castle (Marluxia). Respectably, the last 2 were bosses in their games.
Until some of the later games, every character in Guilty Gear has had their own theme, which plays during battles against them. Certain storyline rivalries have their own themes as well; the theme for battles between Sol and Ky, "Noontide", is practically a theme for the game as a whole.
Whenever Proto Man showed up in the Mega Man games, his appearance was accompanied by a mysterious whistle. In Mega Man 5 his doppelganger Dark Man has a off-key version of the whistle, an early hint that he isn't who he says he is.
The Mega Man Battle Network spin-offs often play a version of each game's theme song whenever a dramatic speech is being made by the main character. Many people were quite disappointed when the theme music changed in the fourth game because it wasn't nearly as suited to those scenes.
The Wily Tower motif in Mega Man 3 has four variations; three for the stages, and one for the bosses.
Also, the Wily Castle motif in Mega Man 10, which has three variations.
Done to death by fighting games, except for the ones that only have stage music as opposed to individual character themes.
By far the most famous examples are the original character themes from Street Fighter II, with Ryu's, Guile's, Ken's, and Akuma's themes quite possibly being the most awesome and prolific music of all. When Final Fight characters showed up in Street Fighter Alpha, they got remixed versions of stage music from the original Final Fight as theme tunes.
SNK has done this as well. Geese Howard's theme names always involve something "for Geese", but all of them are rearrangements of his theme from the original Fatal Fury, which was titled "A Kiss for Geese". Afterwards came "Soy Sauce for Geese" (Fatal Fury Special), "A Kiss for Geese - Cyber Dub Edit" (Art of Fighting 2), "One More Kiss for Geese" (Real Bout Fatal Fury), "A Stiff Neck for Geese" (King of Fighters '96), "Soy Sauce for Geese -End of The First Nightmare-" (Fatal Fury: Wild Ambition), and finally concluding with..."Mustard for Geese" (King of Fighters 2002: Unlimited Match). The only exception to the name rule thus far is "Kiss Geese Once More", from King of Fighters: Maximum Impact. Most games after '96 in which Geese is present have used remixes of "Soy Sauce For Geese", the most recognizable thanks to its flute.
Subverted with Iori Yagami, who had a new theme every game up 'till KOF 2000, but they all had a kickass saxophone solo.
Melty Blood has used the same character themes since its debut. The most prolific ones are "The End of 1000 Years", used for Red Arcueid, and "For Crimson Air", used for Wallachia.
Guilty Gear easily trumps everything else though. Some characters have had the same theme, only differently arranged, from the first game, and every character has had the same theme since 'X', and every  of 'XX' uses the rearrangements from the original 'XX'.
Characters with special relationships often get VS. theme music, as mentioned previously. Guilty Gear XX Accent Core even gave new VS. music to Order Sol and Ky, "Keep The Flag Flying". The King of Fighters '98 gave two different VS. themes to the same fight: "Cool Jam" plays if the player character is Kyo Kusanagi vs. Iori Yagami, and "Esaka Forever" plays if it's Iori vs. Kyo.
The above two traditions continue in the Spiritual Successor to Guilty Gear, BlazBlue: each character has their own unique theme, in addition to "relationship" themes, such as "Under Heaven Destruction" for Ragna vs. Jin and "Imperial Code" for Noel vs. Jin(which doubles as the theme of the organization they both work for). Should come as no surprise: Daisuke Ishiwatari is responsible for the music in both games.
Let us not forget the theme that plays when Carl and Relius Clover fight each other, the depressing and epic, X (Cross) Matic. Also, in story mode when a character appears on screen, their battle music usually plays. (I.E. Rachel is on screen and is not the player character, queen of rose plays.)
Bloody Roar and Bloody Roar 2 for the PS1. You could choose whether the games played stage-specific songs from the arcade versions, or new character themes created for the console ports.
The Sonic Adventure games used leitmotif liberally, having a theme for every playable character or character important to the plot. SA 2's themes for Sonic, Tails and Knuckles used the same lyrics as their themes from SA 1, but used different melodies.
Sonic Adventure 2 really pushed this with Live and Learn; its lyrics, beats, and melodies kept popping up all over the game. Sonic's first stage incorporates "Live and Learn" in the lyrics, the four note decrescendo from the chorus is used in songs such as Supporting Me, etc.
And on occasion, their leitmotifs are changed to a completely different theme. Shadow's has changed several times in particular. At first, he had "Throw it All Away", then he had "This Machine", followed by Sonic Team's attempt to give him six in one game depending on the path you took. Most agree the song "I Am All of Me" was the theme of that game, but the next game he's in decides to say it was the song from the good story of that game, "All Hail Shadow."
Sonic has had to deal with the theme from the original series, then two versions of "It Doesn't Matter", and finally a hojillion (seven) versions of "His World."'
"It Doesn't Matter" has resurfaced triumphantly in Sonic and the Black Knight with two different renditions. Less so, Tails' theme from Sonic Adventures 1 and 2, "Believe in Myself" has been arranged as the theme of the Blacksmith(Who is 'played' by Tails.)
In the original Sonic, in addition to the several versions of Sonic's theme (title screen, game over, continue, ending), Robotnik had two versions of his theme, one during the regular boss battles, the other, more intense version was played during the cutscene at the end of Scrap Brain Act 2, as well as the final battle.
Sonic 3 & Knuckles's mid-boss and main boss themes were variations on a common riff. In addition, there were two different versions of each stage theme for each act, sometimes, as in the case of Lava Reef Zone, sounding almost totally different. And the first half of the main boss theme was Suspiciously Similar Song to Robotnik's original theme(the games had a different composer than the first two).
This was topped by Sonic Advance 3, where each stage theme had no fewer than four variations - one for its map screen plus one for each of the three acts. Somehow it never seemed repetitive, either - the map's theme was more low-key and served to introduce the melodic material, and then each act was a progressively more intense version of the same theme. One of these themes, in fact, was the Green Hill Zone music from the original Sonic; all too appropriate for a stage (Sunset Hill) which was itself a sort of re-imagined and remixed version of that place.
Sonic Unleashed reuses Eggman's instrumental leitmotif from Sonic 2006 and manages to build a new boss music out of it. Speaking of 2006, each villain had his own leitmotif, each with several arrangements for cutscenes and boss battles.
The Zerg get their own little theme in Starcraft II that is made up of two parts; in the Overture, the two play at the same time with the female solo voice doing one part and the low brass doing the second.
The Fire Emblem series actually had a soundtrack release made up of character themes.
Absurd use, in Fire Emblem 9 (Path of Radiance) there's a trio of pirates with their own Leitmotif. Despite them being completely unimportant, to the point that they have less then half a dozen lines among them.
There's also a leitmotif attached to an act. "Together We Ride" is the name of the song that plays when you recruit a new unit in all but a handful of the games in the series, starting from the first game. This one is so tied to the series that it was the Fire Emblem character music in Super Smash Brothers Melee.
Lampshaded in Metal Gear Solid, when Snake actually hears Psycho Mantis's leitmotif play. It's a manifestation of his mind control abilities.
Played straight however with Big Boss's leitmotif. It first plays when he's descending into Russia for Operation Snake Eater. It also plays for his reappearance in MGS4.
In Metal Gear Solid 4, the characters's leitmotifs change in order to reflect their changing personalities. Therefore, it's really alarming when we first see Snake (leitmotif "Old Snake") in his "young" mask, and the music that plays is "Opening Infiltration", his leitmotif from Metal Gear Solid 2 When Raiden reminisces about Rose, his theme tune changes from "White Blood" to "Who Am I Really?", his theme from Metal Gear Solid 2. Naomi borrows her theme from Metal Gear Solid: The Twin Snakes on her first encounter with Old Snake, and later she is accompanied by "Enclosure", Sniper Wolf's theme, when she is in a situation very similar to Wolf's.
In Metal Gear Solid 2, Snake's Theme from Metal Gear Solid plays when the S3 tells Raiden about how putting him through Shadow Moses has turned him into a soldier with all of Snake's gifts. Footage on the screen from the trailers, where Snake was placed into Raiden's shoes during key boss fights, play on the screen.
Ridley in Metroid has had his own fight music ever since Super Metroid. Though it was not exclusively his music in Super Metroid, it has since become identified with his character, much in the same way that the Star Wars Imperial March theme was not intended for Darth Vader himself, yet became his de-facto music nevertheless.
Although not quite so heavily linked to character, the area preceding a boss, (Particularly Kraid) have very memorable themes. This is a given, considering they made the same game twice. (Metroid and Zero Mission).
Samus also got her own theme tune in Super. Notable occurrences have included Prime 3 and Super Smash Bros. Brawl.
Except that what Brawl called "Theme of Samus Aran, Space Warrior" was just Super's Ending Credits tune. In Super, the "Theme of Samus Aran, Galactic Warrior" is completely different.
A truer example would be the little riff that plays whenever Samus emerges from her spaceship/a save station when you start up the game in the Prime series.
That bit is called Appearance, and it's been the customary "loading save/new game start" song since the very first Metroid game.
The Myst games are very fond of doing this, usually having themes for each villain (and for each age, in the later games). Also, Sirrus and Achenar, the evil brothers from the first game, have their themes return in Myst IV: Revelation, if only briefly.
There's the oft-interwoven Saavedro's Theme from the third Myst game and the use of the oboe to represent Gehn in Riven.
In the Star Fox series, the titular heroes and Star Wolf both get their own leitmotifs. Star Wolf's gets a little... over the top in later entries in the series, what with the vaguely flamenco beat and the blaring brass section.
Secondary characters Bill Grey and Katt Monroe both get their own leitmotifs whenever they show up in a level.
In the original, a common leitmotif is used in several of the planet musics, particularly Meteor, Titania, and Fortuna. Several themes are used for different types of boss battles, for example Corneria/Meteor, Outer Space, Venom, and the Atomic Cores(which is a rehash of the opening sequence music), as well as unique BGMs used by the planet bosses.
Hey, come on. The Assault version is really quite epic. Panther joined the group at that point, so maybe they had to Spanish it up a bit?
In Star Fox Command, each character has his/her own background music.
During Star Fox Adventures, Krystal and Fox had their own theme whenever they were on screen together. Given the nature of the two characters, it could be interpreted as a 'love theme'. A longer and more 'tribal' variation of the same theme was used in the Cape Claw location of the game.
Every party member in Tales Of Symphonia has their own theme music, and some have more than one. Zelos, for example, has an upbeat, samba-style tune that shows up when you first meet him, but if you take a certain plot path you'll hear an extremely sombre version of that exact same tune at one point. The Big Bad's theme music is also used for The Reveal at one point.
Quite a number of music in Tales Of Eternia that runs different version of the same motif for Van Eltia and Shileska. Add in all the FMVs one can probably find 20+ of them.
Castlevania tends to use "Vampire Killer" to represent Simon Belmont (from the very first game), although in Super Castlevania 4 he got his own theme music, called "Theme of Simon". Dracula had to wait until Rondo of Blood to get his theme music, "Dance of Illusions". When you fight the original Castlevania bosses before Shaft in Rondo of Blood, the boss music from the first game, "Poison Mind", plays.
And Bloodlines, which first appeared as the music for the first level of Dracula X, seems these days to be affiliated specifically with Richter Belmont's frequent appearances in the games.
Judgment was praised for its music, if not other things, and it took advantage of its fighting game setup to associate its characters with various themes from the series. It may not last, especially as each game introduces new heroes, but there's little reason not to think of "Iron Blue Intention" as Eric Lecarde's theme. Or give "Mad Forest" to Sypha Belnades.
Approach a Trainer (or have them see you) in the Pokémon games and their Leitmotif will play, indicating what kind of Trainer they are. In normal gameplay, they only go on for a couple of seconds, but if you pause the dialogue to listen to the music, you'll be surprised how long they go on for (and how they're arguably better composed than the BGM).
There's also Midna's haunting theme from Twilight Princess, which she is aware of, because she's just that awesome. (Midna's Theme can be heard in at least five tracks from the game, mostly when you're running around areas cloaked in Twilight.)
Saria also plays her own theme song, Saria's Song, and sometimes when she stops playing her Ocarina to speak with Link, the Lost Woods goes completely silent.
And Majora's theme, variations of which are used in each of the four provinces of Termina. And remixes of it are used for each of Majora's boss forms.
Also, Ilia (Link's BFF in TP) and Aryll (Link's lil' sis in WW) have their own melodies, as well as Tetra and her Pirates (though it's replaced as her theme by Zelda's Lullaby once her destiny is revealed.)
The Master Sword has one that plays in some form or another when it is climactically drawn from its pedestal in each game it appears in. You know the one: "Dadadada dadadada dadadada dadadada daaaaah DAAAAAH DAAAAAHDAAAAAH!"
In the Super Smash Bros.. series (specifically Brawl) each series has victory fanfare, however Meta Knight has his own unique fanfare (which is a metalish remix of the standard Kirby fanfare). Due to the music numbering it appeared that pretty much every character would have their own fanfare, but most of them were cut before release.
It is very rare that a game in the Kirby series with King Dedede in it (as in, almost all of them) would fail to have his distinctive theme play when he's fought as a boss. And even if it doesn't play during his fight (or if he's not even fought), it will typically be used as the theme for the Boss Rush-style miniboss tower.
Every character in the Advance Wars series has his or her own theme music which plays during their turn. There's also (in Dual Strike) no less than six different power-up themes; which one plays depends on the power level (Normal, Super, or Tag) and which faction is using it (Allied Nations or Black Hole). If you use a Tag Power with an Allied CO and a Black Hole CO in Vs. or War Room mode, the theme will even change when they switch places.
Super Paper Mario has theme music for certain villains (Mr L, Count Bleck and Dimentio).
Super Paper Mario also features a remix of pretty much every song in it. Most notably, the music for the fight against the Big Bad is remixed during the fight against the TRUE final boss. Bonus points also go to Count Bleck's leitmotif for being a Musical Spoiler: It is a remix of the "Memory" theme.
To a lesser extent, "Inside the Castle Walls" can be considered Peach's theme, as it plays during her appearance in the beginning and ending cutscenes. Toad also has a unique little melody that plays whenever you talk to him.
Characters have their own themes in the Mario & Luigi series, such as Popple's unique boss music in the original, Bowser's Theme in some of the games, Fawful and Midbus' theme in Mario & Luigi: Bowser's Inside Story and probably quite a few more.
Bowletta uses a sped up version of Cackletta's one.
Most major Super Mario Bros. characters have their own theme as of Mario Strikers Charged. A few of the characters had their own themes before that, such as Bowser, Peach, and Luigi. Interestingly enough, Mario only had two before that game, and they were both from games where Bowser, Luigi, and Peach were all playable. Luigi even has two completely different tunes in one of them... one of which was remixed three separate times in that same game.
Also, Pearl's theme is simply a more upbeat remix of Maya's theme.
The "Objection!" theme of each game is considered the leitmotif of the main character; in Ace Attorney Investigations, Edgeworth's "Objection!" theme is a remix of his theme song, "Great Revival".
In the early games, only important characters have their own theme, but in later ones, almost every witness has one.
One example in particular — "Congratulations everyone" pops up in two consecutive games for one character in particular. (she's the only character to have the same theme introduce her) Who is that character? Lotta Hart.
Dahlia has the calm theme Distant Traces of Beauty, and in the end it gets used for Iris as well.
Every boss in La-Mulana has their own boss battle music.
Several characters in Wangan Midnight Maximum Tune:
Akio Asakura: "Blue Blazes" (WMMT 1 and 2), "Phantom of Blue" (WMMT 3)
Tatsuya Shima: "Destination Blackout" (1 and 2), "Black Pressure" (3)
Reina Akikawa: "Nothing Can Live Forever" (1 and 2), "Feel the Moment" (3)
R200 Club: "Decoration for the Dement" (1 and 2), "Evil Association" (3). The latter has the distinction of being played in only one stage of Story Mode.
And in the original Wangan Midnight game, more characters have their own theme music.
RPG Baten Kaitos features Leitmotifs for many characters. The Malpercio has the impressive Ruler Of The Nine Skies. Recurring boss Giacomo uses the very catchy theme Chaotic Dance, which has electric and acoustic versions. In the prequel, a young Giacomo has the remixed Chaotic Dance 2.
Spiriters (or maybe it is the Guardian Spirit itself?) also get their own theme, as implied by Baten Kaitos Origins: The True Mirror, also known as the fancy battle theme music from Baten Kaitos.
Dawn of War features Leitmotif for each of the factions, ranging from heavy drumbeating for the Orks, militaristic marching music for The Imperial Guard to the Asian orchestral of the Tau Empire.
Time Crisis 2 also has General Diaz's theme, which appears in the musics for stage 2-1 and 3-3, the Final Boss battle, and the ending.
Time Crisis 3 has a different theme tune than the other games, but it still uses elements from the original theme, ala Suspiciously Similar Song.
In Left 4 Dead, the three Special Infected (zombies with special abilities) have unique themes that play when they are attacking the players, but the Boss Infected, the Tank and the Witch, have motifs that play constantly whenever they are in the field of play.
There are also quick little riffs that play when one of the three spawn. This builds subconscious associations among casual players and gives hardcore players (the ones who will poke around the games sound files to find these) something to listen for.
Unusually for a western RPG, Planescape: Torment gave leitmotivs to all the principal characters, including The Nameless One, all NPCs and all of the principal villains; all being variants on the same underlying theme used for every piece of music on the soundtrack.
Wing Commander II has a number of prominent leitmotifs, most notably the grim, minor-key brass fanfare accompanying Prince Thrakhath, the syncopated piano motif for Jazz, and the theme that plays during the love scenes between Blair and Angel.
Nearly every character of the large cast of the Touhou Project has their own leitmotif. In fact, many have more than one. This large influx of awesome music fuels not so much the fandom than it displaces it.
There's even a leitmotif for the overall series itself. The unused theme Theme of Eastern Story has been adapted into the opening themes of all the Windows-era mainline shooter games. Particular use was made of the series of running eigth-notes.
Persona 3 and Persona 4 both used this incredibly strategically. No specific character leitmotifs, however...
Persona 3 specifically used about seven different versions of the Tartarus background music, representing the different blocks of the tower. The 'ground floor' rendition ends up more as the main soundtrack to the Dark Hour itself though. More notable, however, is the credits track, Memories of You, wherein musical segments from Your Memories (one of the saddest-sounding songs in the game) and Joy (playing during some of the happiest scenes in the game) are both used.
The game also used instrumental keys from the first verse of "Burn My Dread," and of "Memories Of You," for pivotal background themes. "Living With Determination" is the most noticeable example.
Persona 4 is a little lighter on this. Two different versions of the regular battle theme are used depending on the strength of the enemy. I'll Fight Myself has two versions - one used during major boss fights, and one used for the scenes afterwards.
Elizabeth: Doesn't have a specific theme, so instead the final battle music from Persona 3, Battle Hymn of the Soul, plays instead. Appropriate given she's the most powerful character in the story.
In the firsttwo entries, every party member gets their own theme.
Additionally, 'Poem for the Soul' has been the theme for the Velvet Room since Persona 1; however, 3 is notable for turning it into an insanely rocking boss theme.
Every party member in Mana Khemia and its sequel have a distinctive theme. That way you have an idea of what kind of crazy stuff's about to go down.
Alma gets her own leitmotif in the second FEAR game, which also serves as the game's main theme.
Wild AR Ms games naturally jump on the bandwagon. There's the series main theme, Into the Wilderness, which plays once or twice at key moments in each game, usually the ending or introduction. In Wild AR Ms 1, Boomerang has his own theme, which is slowed down for a "funeral dirge" late in the game. In Wild AR Ms 3, Virginia has "Ready! Lady Gunner!" while the Schroedingers have "There's Only One Family Named Schrodinger". There are special boss themes for Janus and the Prophets.
This is brought to a head for the remake of Wild Arms 1, where each major antagonist has their own theme, and they're all awesome. (Though Zed's new theme is a bit less awesome then his old one)
MMORPG Video Game/Mabinogi has thematic music for each city, most dungeons, and nearly every NPC, as well as the main game theme; variations of which are used in certain cutscenes from the mainstream storyline quests. The soundtrack recordings include about 120 different pieces of music.
In Clive Barkers Jericho, the same haunting piece of music (a lone choirboy, backed by a deeper-voiced choir) plays whenever the mysterious child (who later turns out to be the Firstborn) appears during gameplay (with the exception of the boss fight against it).
Resident Evil 2 had William Birkin's theme, which had a variation for each of his mutations.
Hunk's theme from the 4th Survivor scenario, which becomes more frantic the further you progress.
Sherry, Ada, and Tyrant also had their own musical themes.
* In RE3: Nemesis, the titular monster has many pieces of theme music, but the two most memorable ones are "Feel the Tense...", which plays whenever he is skulking around in the immediate area and is just made to make the player feel incredibly nervous, and "Nemesis' Theme", a much louder and more dramatic piece of music that plays whenever he enters the same room as Jill.
"Never Give Up The Escape", the spooky "empty room" music.
Alexia's theme ("Berceuse") in Code Veronica, which also had different variations for her One-Winged Angel forms.
RE5 gives Wesker a leitmotif, which is heard whenever he appears on screen, and is combined with Jill's battle theme for the song Two versus Two. Interestingly, Wesker loses his theme music when he transforms into his final form.
The first game had the mansion motif, which had different variations for the first and second floors, and further variations when you return to the mansion from the guest house, the haunting "bathroom theme", and also Tyrant's theme near the end of the game.
LucasArts games in general deserve a special mention for developing a special sound engine just to allow the use of Leitmotifs dynamically.
Several exist in the Monkey Island series. Particularly prominent are the themes for LeChuck, the Voodoo Lady, Stan, and Largo LaGrande.
In the Nintendo version of Maniac Mansion, each of the playable characters carried a CD player that basically played that character's theme. Razor's seems particularly popular with fans.
While X-Wing was not the first to use true Leitmotifs in a space simulator (with Wing Commander probably taking that honor), the iMuse system enabled using the various portions of the already huge Star Wars trilogy soundtrack and fitting them almost seamlessly into one another. For that reason, virtually any event that could occur during a mission had its own Leitmotif - to the point where it is possible to figure out roughly how a mission played out just by listening to a recording of its soundtrack.
In the Backyard Sports series, every playable character has their own theme song.
Universe at War: Earth Assault has a different soundtrack for each of the three factions, each with its own theme: the Hierarchy have heavy rock tracks, Novus have a techno/electronica vibe, and Masari have an orchestral soundtrack with plenty of Ominous Latin Chanting. It's worth noting that all the music here was composed by Frank Klepacki.
If a piece of music in .hack has to do with the Phases, whether in the original or GU games, it will feature at least a few measures of a distinct and slightly creepy melody of bells at some point. You can hear it quite clearly about ten seconds into Gorre's original theme: here. The eighth Phase, Corbenik, has his own piano melody across the games, and snippets of Cubia's final music from the first games can be heard in his battle themes from GU.
Piros the 3rd, the Author Avatar of the game's creator, has a themesong involving upbeat tuba music that * ALWAYS* plays over the normal stage music whenever you invite him into your party. Only a few exceptions prevent this: When you're in a Root Town or fighting a Phase boss. No other party character in the game has theme music.
Azure Kite gets "Everything In These Hands" as his theme song. It is both fast-paced and dark, encompassing his mysteriousness and brutally efficient fighting methods, but also contains a calmer section reminiscient of Mac Anu's music, hinting at his true nature.
Several romantic scenes in G.U. have "Shino-Honeysuckle" playing in the background.
Also, every time you see Ovan, "The Epitaph is Told" plays.
Most funny scenes (excluding those with Piros) have the song "Troublesome Girl", which may or may not be originally intended more-or-less for Atoli, hence the "girl" part of the title.
Syphon Filter: The Omega Strain has Logan's theme; a variation of the main Theme Tune, the Agency theme, Aramov's theme, Theme of Zeus, and Theme of Metaglobal, and each terrorist group has a characteristic battle theme.
The melody of the main theme from The Witcher can be heard in several other tracks, both event specific and general background music.
In Cave Story, Quirky Miniboss Squad-member Balrog and Big Bad The Doctor each have their own theme that plays during their cutscenes: "Balrog's Theme" and "Tyrant" respectively. There's also "Jenka" which first pops up in Jenka's house, then serves as the music for the Labyrinth—this is the first clue the player is given that Jenka figures big in the island's backstory.
The soundtrack to Mother 3 is very heavily built on leitmotifs that recur in numerous variations over the game, including His Highness' Theme for scenes about the Pigmask Army, the saxophone line in Magypsy's Home, Sweetie-Pie for the Magypsies (which actually serves as a Musical Spoiler later on in the game if you're paying attention), and, of course, the Love Theme, which will break your heart with its every appearance in the context of the game.
It could be argued that each enemy has a Leitmotif, however some enemies share the same theme. That said, with there being 250 soundtracks, most enemies (and bosses) have their own themes.
EarthBound's Dragon Pokey has a theme that follows him everywhere as do The Runaway Five, and the Sound Stone melody also acts as one for Ness and the journey as a whole after you've found all of its pieces. Paula also has a Leitmotif, but it's not heard as often.
In Mass Effect, the Normandy and Commander Shepard share many of the same musical cues and riffs in their respective themes, appearing in all three games, suitably heroic sounding for both of them. The second game features a variation of this theme called "Suicide Mission", appropriate for the game's darker tone. Shepard in particular has a recurring violin and brass riff associated with them, noticable in "Spectre Induction", "The Normandy Reborn", "The End Run" and "The Fleets Arrive".
Saren's leitmotif in the first game also doubles as the "Critical Mission Failure" music, subtly conditioning the player to hate him throughout the entire game!
"Vigil" from Mass Effect. In the first game it plays during the startup menu and when Vigil himself appears to tell you the fate of the Protheans, Sovereign's plan, and how Shepard can stop the Reapers from returning. In Mass Effect 2 it plays when Shepard briefly reunites with members of his squad from the first Normandy: a reminder of the sense of wonder the first game held, in direct contrast to the second game's much darker feel. It plays again in Mass Effect 3 after the genophage is cured, finally giving the Krogan hope, and when the Geth and Quarians reunite, if you managed to convince them to make peace. You can vaguely hear it in the War Room as well. And finally, it plays during the Distant Finale with the Stargazer telling Shepard's story to a young child.
In Mass Effect 2 the Collector ship that destroys the Normandy and kills Shepard has a distinct percussive, syncopated leitmotif that appears in every single track that features the Collectors.
Likewise it's been twisted and deepened but if you listen carefully you can hear Vigil's theme almost buried in the background of the collector's theme, hinting that the Collectors are Reaperised Protheans.
The soundtrack to the Kings Quest IIFan Remake uses these to powerful effect. The soundtrack remixes and gives full MIDI treatment to not only music from the original game, but weaves in musical references to other games in the series at the Air Gem tests. It uses a couple internal ones, like an instrumental version of the Award Bait Song for Valanice and integrating Grandma and Possum's themes when Graham is confronting the vampire.
Fallout New Vegas lacks a defining lemotif track, but actually has 2 different entire soundtracks depending on your karma. If you do evil stuff, you get a dark brooding soundtrack, if you do good actions, you get an upbeat heroic sounding soundtrack.
In the Dead Money DLC, Dean Domino seems to have "Something's Gotta Give" as sung by Bing Crosby as his theme.
Don't forget the one cello note for the radio "communications" coming from the Rapture leader.
The Ys series has several, eg "Theme of Adol" and its remixes, "Feena", "Lilia", "Theme of Chester", "Karna", "Leeza", "Eldeel", "Niena", "Theme of Lovers"(Stoker's theme), "Theme of Kefin", "Olha", "Successor of Almarion"(Ernst's theme), "The Depth Napishtim", etc.
Basically, every Rare videogame has its own recurring main theme.
Banjo-Kazooie series has two main motives, along other recurring themes, Banjo-Kazooie Main Theme, which appears in tracks such as Overture of the three main games, first game's Final Battle, Cloud Cukooland; and Gruntilda's lair, featured during the final battles and in tracks like in Grunty Industries or LOGBOX 720. Both also appeared in many games' cutscenes.
Conkers Bad Fur Day has some recurring themes, the most famous is "Windy", played in the hubworld and in musical tracks such as "Barn Boys", "Give us our money back, honey" and "The Ugga Bugga's". Ze professor Von Kriplespac's theme is played during the battle with The Little Girl, when Conker is in the Windy's harbor and during the second assault in the remake.
Live & Reloaded, remake of Bad Fur Day, also features a recurring theme, that plays during the game intro, and briefly as game over in the Chapter X, as well as in "Doon I" and in "The Ditch".
Dead Rising 2 used a guitar riff associated with Chuck Greene, and in the final-final boss battle an extended version of the riff is played for the fight theme. Both the riff and the fight theme can be classified as Crowning Music of Awesome.
Wolverine is an interesting example of this, as up until Marvel vs. Capcom 3, he had five different themes; a new one for each game he appeared in between MSH, X-Men: CotA, XvSF, Marvel Super Heroes Vs Street Fighter and MvC1. 3 was the first game to actually remix a theme of his. Some of the other X-Men characters got different themes for each game they appeared in, as well.
Actually, all of Wolverine's themes are arrangements of his theme from X-Men: Children of the Atom. It's just that it's been so heavily remixed with such different tones each time that people who casually listen to each arrangement will miss it. This is also the case with all of the other X-Men characters' themes (Gambit and Omega Red are the only exceptions) prior to MvC2. In the case of Wolverine, Hideyuki Fukasawa (the composer of MvC3) took the original MvC arrangement of his theme and made a more straightforward remix of it.
Nearly everyone has one in Getter Love!! To quote the review:
A wide array of musical styles are present in Getter Love, and the songs match the personalities of the girls and the feel of the game to a tee. The popular cute girls [Ayumi and Natsuki] have peppy cheerful J-Pop tunes (luckily without the vocals). The classy girl [Makoto] has a smooth, jazzy piece, and Shizuku, whose name means “drop of water”, has a song that is serene like a trickling stream in the woods. My favorite song, belonging to my favorite girl Kiiro, has an almost Hindi feel to it complete with chanting melodic vocals. For those fond of Asian music, Meifa is stereotypically given a traditional Chinese song, gongs and all.
All of the characters in Team Fortress 2 have at least one. They are as follows:
Heavy: The main theme (simply titled "Team Fortress 2"), as he's almost the main character of the game.
Soldier: "Rocket Jump Waltz", "The Art Of War"
Engineer: "More Gun" (based on Wilco's "Someone Else's Song")
Call of Duty: Modern Warfare had a particularly striking one used throughout the game (composed by Harry Gregson-Williams, which was sadly ignored by later composers for the series.
Too be fair, Modern Warfare 2 also had multiple striking Leitmotifs, such as the Opening Titles, Contingency (TF 141's theme), Extraction Point (Ranger theme), and the distinctive climax heard during Guerilla Tactics (Militia theme). Safeguard is also used for two notable chase sequences, the Snowmobile escape and the Jeep escape.
In perhaps one of the first video game leitmotifs, Baron Von Blubba in Bubble Bobble is always accompanied by a short, ominous riff whenever he appears on screen.
In Star Control, at the end of each battle, the game would play a short "ditty" specifically belonging to the winning ship's species. This went much further in Star Control 2 where each (of over 20) species got its own theme music, accompanying any interaction with members of that species.
Ace Combat: Assault Horizon has its own main theme song, "Gotta Stay Fly", which has a variety of brief and major appearances throughout the game, either in the rock portion or the orchestral theme. It is most notably used during Bishop's nightmare, then a different version when he actually is over Miami reliving his nightmare for real and facing it anyway, and finally the full song over the end credits.
Markov has a bit of his own leitmotif, a sad song that plays when he is first introduced and in full during your last dogfight with him. Its title is "Mrs. Krista Yoslav", who is kind of important. She was Markov's wife, who was killed by a botched NATO bombing run, leaving him a Broken Ace who just wants revenge. She is his leitmotif.
In the Soul Series, Maxi's theme appears to be Sail Over the Storm. It's used in both the first and third games, and the first 10 or so seconds appear again in the fifth game.
In The Elder Scrolls V Skyrim, the main character is a Dragonborn, and his leitmotif is suitably named Dragonborn. It plays as part of the main menu screen and, for added awesomeness, it often plays when a dragon attacks the player providing a nice musical backdrop for an epic dragon fight.
Every character in Puyo Puyo Fever's 15th Anniversary gets some sort of Leitmotif. In Fever 1 and 2, a special song plays during the cutscene before facing the final boss; Phony Demon King for Popoi in Fever and Resurrection of the Ancient Spirit for Strange Klug in Fever 2. In the Normal Course of Fever 2, you hear this before facing the boss, Lemres.
Most legendary Pokemon, or groups thereof, get their own themes that get played even when they cameo in later games: there's a theme for every minor legendary trio in the second through fourth generations, and a theme for every Pokemon (or group thereof) that appears on the covers of the games. Also, the games based in Sinnoh had a generic legendary theme that plays for various legendaries. As most of them got different themes later (or in Darkrai's case, was event only, or in Rotom's case, wasn't really legendary to begin with), Black 2 and White 2 use the theme as Heatran's leitmotif.