The different areas of the Incipisphere now each have themes ("Doctor", "Endless Climb", "Atomyk Ebonpyre", and Frost for LOWAS, LOLAR, LOHAC, and LOFAF, respectively). Jack Noir's theme is "Black". Most of the Trolls were given their own character themes in the "Alternia" and AlterniaBound albums, but not all of them have been used in the comic itself.
"Doctor" has since become something of a Bootstrapped Theme for the God Tiers, by way of its remixes "Savior of the Waking World" (used when John ascends in Act 5 Act 2) and "Savior of the Dreaming Dead" (used when Jade ascends in [S] Cascade).
Terezi Pyrope's theme, "The Lemonsnout Turnabout" is a dual example: not only it's her theme, but it uses its instruments - according to the composer's commentary - to tell a story where the oboe is the accused Senator Lemonsnout and the harpsichord is the prosecutor Terezi. Therefore, it also uses a leitmotif in its more traditional sense.
"Sburban Jungle" acts as a leitmotif for Sburb (and is apparently the music that plays on Sburb's loading screen). Other tracks associated with the game as a whole include Homestuck Anthem and Homestuck for the Kids, with "Theme" *
Rex Duodecim Angelus is the music for the Trolls' Boss Battle against the Black King. In addition to the Black King's theme, the themes for the Trolls are played as they join the battle. The commentary in the PDF expands upon this idea further, laying out the scene as the music progresses.
Then Descend combines them all together into one big ball.
More subtly, The Carnival is associated with clowns and harlequins. It makes its first (8-bit) appearance with John's kernelsprite, though the full version isn't unveiled until the showdown with Gamzee.
Many of the characters have associated instruments as well. The kids all have one, as do Terezi (harpsichord), and Vriska (electric guitar). The most extreme is probably Gamzee and his horns- in fact, his section of "Rex Duodecim Angelus" is not actually his leitmotif, it's the Black King's theme played on horns, mocking him.
More recently, we have Eternity's Shylock (linked directly in-comic), which serves as a leitmotif to Caliborn, who is strongly hinted to be a young Lord English, and the title isn't doing anything to dispel such notions...
Homestuck even goes so far as to use the concept of leitmotifs as a combat technique, with each aspect and combination of aspects having one or more "fraymotifs" available to fight with.
