The different planets of the kids' Incipisphere also have themes ("Doctor", "Endless Climb", "Atomyk Ebonpyre", and Frost for LOWAS, LOLAR, LOHAC, and LOFAF, respectively). Each theme also functions as a secondary leitmotif for that planet's associated kid.
"Doctor" has 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).
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.
Terezi Pyrope's theme, "The Lemonsnout Turnabout" is a dual example: not only is it 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 leitmotifs in the more traditional sense.
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.
"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" note a bonus track on the Alternia album and Alternia for the Trolls.
Harlequin is a theme associated with clowns and harlequins. It makes its first (8-bit) appearance with John's kernelsprite, but later versions accompany other harlequin-themed things in the Medium and The Carnival is a dark version that plays along with the showdown with Gamzee.
English is the theme for Lord English. It is prominently featured in Eternity Served Cold, the piece played when Caliborn frees himself and enters the Medium, as one of many.many hints that Caliborn is a young Lord English.
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 clown 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.
Long story short: pick a character. Any character. Chances are they'll have their own theme song, if not more than one.
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.