The elevator in Titans Tower is plastered with stickers of the faces of various heroes, villains, and iconic symbols. Among some of them are the Bat symbol, The Joker, the Green Lantern symbol, Wonder Woman's icon, and more.
This is a reference to the fact that the original series wasn't allowed to directly name or show characters being used in Justice League. This is certainly not the case anymore.
In "Legendary Sandwich", a cardboard cutout of Batman is advertising a cereal named "Bat-O's" when Robin is in the supermarket.
Also behind the deli counter, you can see Joker has been named Employee of the month.
Nightwing's fridge has another Batman sticker. And a half-eaten Batman-branded cupcake.
The defendant that Beast Boy proved guilty was Ed, the criminal/Driver's Ed instructor who was later seen in "Driver's Ed".
In the "Driver's Ed" episode, a club is featuring DJ Aqualad.
And later, we see the Jonah Hex Casino, featuring a live performance by Mumbo Jumbo.
Not too long after that, the Titans (minus Robin) are chilling outside a coffee shop called "Justice Java," with a picture of Superman on the sign.
The stuffed animals on Starfire's bed in "The Date" are dressed as various DC characters, including Wonder Woman, Green Lantern, Batman, Robin, Flash and Bane in his The Dark Knight Rises costume. In "La Larva de Amor", Robin puts them back on her bed while looking for Silkie, also in a split second.
There's also the Darkseid plush seen sitting at the foot of the couch in several episodes.
Some of the posters in Raven's room feature Etrigan and Ra's Al Ghul.
The tub of ice cream in "Double Trouble" has Mr. Freeze on it.
Trigon flies a Pretty Pretty Pegasus kite near the end of "Dog Hand", visible in a wide shot and for two frames in a close-up before it's disintergrated. Seems that liking the show runs in the family, given Raven's behaviour in Legendary Sandwich.
The boy whose nightmares Raven takes in "Dog Hand" has a poster of Doomsday over his bed.
Silkie zips through an underground chamber adorned with Batman crown moulding. It contains an ancient Egyptian style Ra's al Ghul sarcophagus and canopic jars with Catwoman lids.
Silkie passes by two guys fishing on a boat. Except it's not just any two guys, it's Batman and Commissioner Gordon. And it's not any boat, it's the Batboat (roughly looks like the one from the 1966 movie).
Beast Boy found a box of Bat-O's in the kitchen cabinet, much to his delight.
During the montage of Silkie and his girlfriend, they smash open a pinata shaped like Krypto the Superdog.
In "Hey Pizza!", the dollar bills have Lex Luthor's face on them.
There's a toy store with Alfred the butler on its sign. When it's destroyed, his smile turns into a frown.
In "Girls Night Out", Cyborg imagines himself wearing the Riddler's hat.
Batman and Commissioner Gordon are on a stakeout when the cops are chasing the girls.
In "The Date", Bane, Doomsday, and Slade are on Robin's punching bag.
In "You're Fired", people keep calling the front desk at Titans Tower, asking for the batcave.
A picture of Raven without her hood can be seen behind Zan while he's a receptionist.
In "Super Robin", Beast Boy's transformation into a T. Rex can be paused at the right time to see him as a human/dinosaur hybrid.
When Robin gets bored in his new job, he draws a long dragon with Joker's face, and shoots a bat-symbol on the wall with staples.
Batgirl, Aqualad, Bumblebee, Más y Menos, and Speedy can be seen at the party in "Starliar". The latter five are from the Titans East, organizers of said party.
When Cyborg is presenting a powerpoint about burgers, you can see a burger diagram with a question mark next to the patty. In other words, he doesn't know what veggie patties are made of.
In the opening scene of "Waffles," Robin is reading a newspaper with the headline of: "Batmobile lost a wheel!" and beneath it: "Joker got away." This is a pretty great nod to an episode of Batman: The Animated Series, where the Joker sings his own version of "Jingle Bells."