Actor Allusion: Javert at one point is "being John Malkovich"; Elizabeth is very weirded out by seeing Sweeny Todd and Legolas; Rorschach mistakes Raoul for Nite Owl.
Beyond the Impossible: The main reason Chihiro is the unofficial president of the Wibsy (Weirdo Boyfrend & Supernatural Stalker club): using Christine words "It's hard to trump dating a river." While the others have at least human-shaped (a fae, a ghost and a vampire amongst others. Christine with her murderous deformed psycho is the most normal of them all.) boyfriends/stalkers, so this is impossible by their standards. in her defense the river was in the form of a human boy that looked her age at the time she fell for him.
Sarah, for whatever reason, has a video copy of her movie.
Christine has mentioned the largely fan-reviled proposed sequel to ALW's musical.
Brick Joke: Back in comic #35, Sarah wrangles a promise from Erik to wake her up if she's ever found wandering towards a certain person's room in her sleep. 2 years and 93 comics later, she gets a rather rude awakening.
Cuteness Proximity: Jareth uses his owl form as a means to get close to Sarah on occasion, when she doesn't react to the sad fluffy owl on her windowsill he knows he's screwed up big time.
Cut His Heart Out with a Spoon: Here Jareth threatens Erik with magicking all the songs of Miley Cyrus into Christine's head if he doesn't let Sarah go. Later he uses a rather elaborate threat how he'll stop Webber before he makes the musical (leaving Erik with only his literary characterization). There are also frequent threats of boging (meaning: "Headfirst into the bog of eternal stench" or something like that) from either Jareth or Sarah.
Dramatic Irony: Sarah has a crush on David Bowie, while Christine has a crush on Leonidas, but could very well have a crush on Gerard Butler. If you don't get the joke, look up the actors of their respective stalkers.
Almost Lampshaded when Christine thought it was weird that Sarah likes him, but can't understand why.
Dramatic Wind: Jareth likes to conjure one of these up now and then. Particularly when he's trying to convince Sarah to team up with him in a game of Risk.
Failure Is the Only Option: The Apartment has a fail field surrounding it, so anything that should be awesome... isn't. Like when Edward Cullen happened upon the Barbecue for Toby's birthday...
Fourth Wall Observer: Aziraphael and Crowley, to the point that they essentially call out the comic on being too meta in one strip.
"[Aziraphael and Crowley are] having a long and convoluted debate about whether wiping his memories of today would be a good or a bad thing. If they come to the conclusion that it's a kindness, Azi will take care of it. If they decide it's wrong and deceitful, Crowley will."
The next time Raoul is subjected to this, Christine only comments on the potential health risks a second mind wipe may or may not cause.
Love Triangle: Triang Relations type 4, possibly type 7 between Raoul, Christine and Erik. Also, pretty much any guy Sarah wants to be involved with besides Jareth. Look, there's even a quadrangle!
May-December Romance: Played with as the characters lean on the Fourth Wall. Jareth is a fairy tale kind from... a long time ago. Sarah is in college... and was 15 in 1986, and had at least one date with Jacob Black, definitely a teenager.
Medium Awareness: Outside of the occasional bout of fourth wall breakage, the characters are seemingly aware they're in a humor comic, and will sometimes comment on it.
Naughty Tentacles: this comic. Notable because its title is "The Tentacles Trope," and the author links to this wiki.
Never Wake Up A Sleepwalker: Erik advises Sarah not to wake Christine when she finds her sleepwalking toward his room for some late-night music lessons. Sarah dryly informs him that modern science has disproved that notion, then makes him promise to forget the potential trauma and just dump a bucket of cold water on her if he ever finds her sleepwalking toward Jareth's room. See Brick Joke for the follow-up.
Of Corsets Sexy: Jareth catches Sarah while she's playing dress-up in Christine's undergarments. That particular comic page is a fan-favorite, having spawned at least one fic on Deviantart.
The off-screen fight between Jareth and Frank-N-Furter, which many readers imagine to be an epic thrown-down of glittery madness.
Erik's "plan" to thwart Jareth during the kidnapped Sarah arc. Said plan included the use of salt and deadly black chikins, of which Jareth is known to be very afraid of.
Jareth's planned fight against Peter from Heroes for Sarah's love.
Those last two are more of a Missed Moment of Awesome seeing as they never happened instead of simply occurring off screen.
One of Us: Pika is an avid Troper, as shown on many of her artist's comments
Otaku: It's rarely touched upon, but Erik likes anime. He once tried to get Christine to dress as Sailor Moon for Halloween.
Tangled Family Tree: Jareth's inexplicable relation to pretty much every magical blond in fiction (Jadis is his mom, Nuada is his nephew, Howl is his great great great great grand-nephew once removed...) is something of a Running Gag. This comes from Roommates. In the "Building-verse" every magical being is related somehow, not just the blonds.
Tempting Fate: Sarah actually invokes the trope so it'll be subverted when she decides to rummage 'round Jareth's room, since doing so makes it predictable and thus not funny. It doesn't work.