In nearly every episode, but taken to the extreme level in "Night of the Huntress!"
"Menace Of The Conqueror Cavemen!": Kr'ull seems to have an...interesting reaction to turning his girlfriend into a cavewoman.
In the cold open for "Inside the Outsiders": every single line of dialogue between Batman and Catwoman. Taken to new heights when Batman mentions he should "collar" Catwoman with a crafty smile. At the end of a short scuffle, he then ties her up with her own whip. Ooh, Batman, you kinky man, you...
At the end of that episode, it isn't said what "happy thoughts" Batman used to defeat Psycho Pirate, but given the way said cold open ended...
Wonder what the Birds Of Prey would sound like doing a swing number about the sexual inadequacies of the DCAU's superheroes? Behold!
This actually didn't get past the radar, to an extent. The episode has never aired on US television, the bit with Huntress wiggling her pinky in reference to Aquaman was edited to a simple index finger wag after the initial airing, and the episode wasn't released with the rest of the season two DVDs (but was released with season three).
But other countries such as Australia left the episode unedited.
And then there's the other reason the episode didn't air: Batman gets gunned down by mobsters. Several times. With realistic guns. Of course he gets better, but still...
In "Aquaman's Outrageous Adventure!:"
Blue Beetle(regarding Planetmaster): You really don't wanna see the power of Uranus.
"Clash of the Metal Men!" has Platinum turning into a chair for Batman with her face being the seat. Not to mention her common Double Entendres.
Episode 12 of Season 2 brings us this:
Detective Chimp: Well, hello there. I don't believe we've had the pleasure. I'm Chimp. Detective Chimp. Vixen: B'wany, combine him with something, so we can escape. Detective Chimp: I'd rather he combine you and I, my dear. We'd make quite the couple, don't you think?
"A Bat Divided!"'s Slacker!Batman is very reminiscent of a stoner. He even claims a case of the munchies!
"The Criss-Cross Conspiracy" has to be the gayest Batman story ever. Among other things:
It gives us this little gem when Batman switched bodies with Batwoman and tries to free himself from being tied to a chair. He miscalculates and falls over chair and all.
Batman: "Apparently, my center of gravity is now much... *throws glance at his/her chest* ... higher."
Batwoman (in Batman's body) checks out Nightwing! Then she asks him if his cape "made him look fat!"
Batman (in Batwoman's body) has to flirt with Felix Faust to get his help.