The circus flashback itself is a reference to Dick Grayson, the original Robin in the comics. This is in line with a previous reference to the circus in the original Teen Titans series when Raven entered Robin's mind, suggesting that the Robin in the show is the DC Animated version of Grayson. It should be noted that the episode baits viewers who know this into predicting that Robin stopped relaxing after his parents were killed just like in the comics, only to reveal that it's because the animals kept stealing his stuff.
In "Laundry Day", one of Cyborg's bodies is shaped like one of the Voltron lions in leg mode.
When Beast Boy uses a vacuum to suck up Cyborg's soul, the music resembles the Ghostbusters theme.
Starfire's dress-making skills and the end result is a lot like what the character Giselle does for a hobby in Enchanted.
When the suits start attacking, Robin's and Raven's suits slack off and dance to the "Yeah! Woo!" loop.
At the start of "Ghost Boy", Beast Boy pops out of Robin's closet as a Velociraptor using the Jurassic Park T. Rex's roar.
"La Larva de Amor" has several during the milk mustache contest, such as Robin becoming Mario, Raven becoming Gandalf and Beast Boy becoming Chewbacca, complete with Bowcaster. Also, Cyborg resembles B.A. Baracus.
Of the many references to other DC characters in the series, perhaps the most potentially impactful on the story was Beast Boy finding a Green Lantern ring in the couch at the start of "La Larva de Amor". Of course, as he was looking for something else, he tossed it aside.
Apparently the skeleton reaching for water under Starfire's bed was Deadman (Boston Brand).
He later talks about Webster and The Pointer Sisters.
He mentions that the actor who played Webster "was like 40 in real life". Cyborg may have confused him with Gary Coleman, who starred in Diff'rent Strokes.
When Cyborg is hooked up to the Titans Tower mainframe, he loses his humanity and starts acting more like HAL 9000. He even starts speaking in a Creepy Monotone, only shows his cybernetic eye, and utters the famous line "I'm sorry, but I cannot do that".
He also starts filling the Tower with a green gas that looks like the neurotoxin from Portal.
In what may or may not be an accident, Raven's shoes contain one skull each in the exact same design and color scheme of a popular hentai artist's logo who has done two Raven flashes and several more Teen Titans flashes of the other characters. For obvious reasons, links will not be provided.
When attempting to communicate to Cyborg via pictures, Raven draws Darth Vader's helmet to represent "force". For clarification, the message, in this particular case, is that Cyborg always force her to have a good time.
One of the ponies Raven plays with has a blue mane and pink fur, like Firefly from generation 1 of My Little Pony. Firefly happens to be the favorite pony of Lauren Faust, who created Friendship is Magic, where Raven's voice actress, Tara Strong, plays the lead pony.
Robin's flashback in "Baby Hands" has all the Titans in their original outfits.
In "Caramel Apples", there are quite a few:
Robin's inspirational speech to Cyborg and Beast Boy when they're trapped in Hell is rounded off by saying, "...and most important, HEART!" It serves as an Actor Allusion for Scott Menville, his voice actor.
Control Freak being a male fan of Pretty Pretty Pegasus is a Shout-Out to Bronies.
A little later, Starfire hits him with a Shoryuken.
When the Titans are transported to the Pretty Pretty Pegasus show, Raven's face resembles the "Awesome Smiley"◊ as she floats off screen.
The first few notes that play before the Pegasi start the "Friendship Song" resemble the main theme of Tiny Toon Adventures. Also, when she's about to sing, Sparkle Face's eyes begin to cross extremely similarly to Pinkie Pie when she did it in the My Little Pony: Friendship Is Magic episode "Party of One".
In "Salty Codgers", the gravestones during Death's Musical number include Boston Brand, Jason Todd, Martha & Thomas Wayne, and Zod.
In "Thanksgiving", the Imagine Spot used to illustrate Beast Boy's explanation on why there are more rats resembles a scene from the 1947 Disney cartoon Pigs Is Pigs, replacing the Explosive Breeder Irish jigging guinea pigs with the rats.
In "Boys vs. Girls", Beast Boy briefly morphs into the mutant motorcycle rider on the cover of The Ramones final live album We're Outta Here!