You could even argue that the entire style of the show itself is loosely based upon FLCL and it's stylization.
"257-494" ("Don't Touch That Dial") is pretty much twenty-two minutes of references. They even got in the Star Wars Kid Most notably, the climax is an extended parody of The Empire Strikes Back..
"Fear Itself" is the introduction of Control Freak, as well as some awesome Star Wars and Star Trek references. Not only is Control Freak's sole reason for attacking a video rental store because he found out that they had not made 'Warp Trek 5'(with the original cast from the TV show!) one of their top suggested movies to rent, starring an alien with pointy ears, the sound his remote makes is the same sound the transporter makes. He even calls the salesgirl a tribble! He then goes on to assure that although the Teen Titans are not afraid of him, they will be soon by quoting Yoda.
Look hard at Thunder and Lightning's style, their artwork resembles Osamu Tezuka era Anime character models, and for that matter, look at how stylized the episode in general was, if I recall, when Beast Boy lectures Thunder for the second time, it looks similar to Japanese Mythology (Appropriate, considering how the designs and mannerisms of Thunder and Lightning resemble Japanese legends), and the end of the episode, look at the horizon, it's also very stylized.
In "How Long Is Forever?", the punks tormenting Beast Boy have similar designs to the Mutants. Coincidence?
Beast Boy briefly turns into Chewbacca in "Stranded". Then later carries Cyborg as if he were C-3PO!
Immediately after the Chewbacca shout-out, he turns Cyborg into Giant Robo (and himself into Daisaku Kusama)!
Watch just after the first commercial break in "Fractured"; Larry turns Robin's arm into a chainsaw.
Possibly jumping the line between homage and plagiarism, the episode "Car Trouble" copies the entire minutes long chase scene from The Castle of Cagliostro, down to the level of detail visible in each shot.
In "Betrothed", the scene where Robin yells Starfire's name through a glass window is very reminiscent of The Graduate.
What about the fact that Robot Chicken made a parody of the show? Then not long after, in "Stranded", Beast Boy accidentally rebuilt Cyborg as a chicken? Even funnier when you know that the creators of Robot Chicken have credited Cyborg as the basis for their Chicken design.
The inside of Kitten and Killer Moth's house is suspiciously similar to the house from The Brady Bunch.
Inside?!? Suspiciously?? There's a shot of the outside, and yes, it's very much The Brady Bunch house, right down to the landscape in the back.
Robin's discovery of the real appearance of The Chessmaster, Mad Mod, is a shoutout to the Cowboy Bebop episode "Bohemian Rhapsody" where the Big Bad is found to be a decrepit old man playing chess.
"Revolution" has several Monty Python's Flying Circus references, including: shrill old women discussing shopping, the Terry Gilliam look of the illusions he uses, and, of course, a giant foot crushing all of the team except Robin.
It is also a constant reference to the "Eleanor Rigby" segment of Yellow Submarine: The newspaper cutouts which replace the city mirror those used for Liverpool.
The design of Red X◊ is very similar in tone, motif, and look to Skull Man. It's a bit tough to call, though. Skull Man does predate this show by a lot, but that specific design didn't come until the 2007 version by Bones.
Brain's robot body and voice in "Homecoming" suspiciously similar to that of a Dalek.
This was intentional, funnily enough.
In "Calling All Titans" he says "Shall we play a game?" possibly referencing WarGames
In the last episode of the fifth season, "Things Change", a kid who resembles Napoleon from Napoleon Dynamite is also attending Terra's school and can be seen passing by in front of the camera in a few scenes, notably in the library and at the end of the episode in the hallway.
Adding to this is the fact that, in the school's hallways, posters reading "Vote for Pedro" can be seen.
In the new short "Movies" Control Freak is painted as a Navi from Avatar riding a mecha suit from either the same movie or Aliens, which appears to be the movie the Titans are watching.
The computer virus Cyborg is infected with in "Crash" is clearly Keramon, the baby form of the Big Bad of the second Digimon movie, Bokura no Wargame.
Ho boy. In the New Teen Titans short "Turn Back The Clock", Mad Mod is turning back time with a red TARDIS. As time goes backwards, the teams' costumes go through their previous iterations from the comics, including pants-less Robin and Stripperific Starfire. When they reach the 70's, they get the costumes from the Scooby-Doo gang, complete with B.B. Snacksnote (This also dual wields as another shout out - there WAS no Teen Titans in the 70's!) When Robin cranks time forward too far, he's turned into "Robin the Toy Wonder" from DC One Million; the other four titans are replaced with the futuristic heroes of Titans: Scissors, Paper, Stonenote (an Elseworlds series by Empowered author Adam Warren), with the designs done by the series' character designer Derrick Wyatt for fun in 2006 (which helps explain why "Witchie-Poo" looks remarkably like a post-upgrade Sari Sumdacnote (Another series with designs by Wyatt).
Not to mention the opening animation of the sun & Big Ben is straight from Yellow Submarine.
The ending animation where Mad Mod is having trouble keeping up with the conveyor belt is reminiscent of the ending credits from The Jetsons.
At one point during "Transformation" the T-Ship gets eaten by a planet, and the Titans then escape in a manner reminiscent of the asteroid escape from The Empire Strikes Back.
At one point in the episode "Sum of His Parts", Robin's 'locator' sounds literally identical to the Star Trek: The Original Series' communicator. And, to cast aside any doubt, it looks oddly similar, too.