Only one time, and nothing sexual, but when Arrowette and Wonder Girl's moms found out they went on a co-ed camping trip with the boys, they flipped their lids and went to give the girls what-for... only to find them asleep in their own tent, holding hands, with Secret in mist form hovering asleep around them.
Batman and Superman suspiciously appear like the parents for Conner, with Superman as the deadbeat father, Superboy as the son who wants his father's approval and Batman as the single "mom" trying to get the father and son to reconcile. Twice, Batman pulled Superman aside because he wanted to talk to him about Superboy. Not to mention the whole "date" they had while in their civilian identities.
Downplayed in season 2 when in Alienated we learn that Superman and Superboy are now on good terms but they act more like brothers than father and son.
Green Arrow and Sp—Red Arrow seem to have SOMETHING going on. When Roy appeared for the first time as Red Arrow, there was something oddly awed about the way Ollie says to him "Roy, you look...". Roy responds with a curt and jealous sounding "Replaceable!" when he sees his former mentor touting Artemis as his "niece" and new protege. He even starts doubting her abilities to her face. "I thought I was his partner", indeed.
As of "Terrors," we have the Icicle Jr./Superboy and Killer Frost/Miss Martian.
It's subtle in a blink and you miss sort of way, but Frost was watching as Miss Martian was changing.
Junior and Superboy have much better chemistry than Miss Martian and Superboy.
Artemis and Megan have a fair share of Foe Yay in their first episode. Come the next episode and they're like sisters.
In "Performance", Conner uses the shields Lex Luthor gave him in order to regain his powers after they're stolen from him by The Parasite. When The Parasite proceeds to steal them again, we get this line:
Parasite: Ohhh, what a rush! How do you do it, kid? Even Superman couldn't recharge this fast!
Remember this line by Lex Luthor? "You'll provide your services, but for free? I can live with that, hero." Complete with shoulder touch and eyebrow quirk... taken out of context it sounds downright pedo-bear. Maybe Luthor liked having Red Arrow on the case a little too much?
Even worse when you realize he's seen the real, 15 YEAR OLD Roy Harper in nothing but his underwear and has pretty much kept him in his freezer for the last three years at this point. If the above wasn't pedo-bear enough. His interactions with Red Arrow become much creepier with this in mind...
It's easy to see Kid Flash as having a crush on Red Arrow, considering how much he tolerates Red Arrow's consistently rude behaviour, expressing constant excitement about the prospect of Red Arrow joining the Team, and, most tellingly, holding a season-long grudge against the very attractive female Artemis for "usurping" Red Arrow's place on the team. The same applies to a lesser extent for Robin and Aqualad, who consistently refer to Red Arrow as one of their dearest friends despite him being nothing but rude to them. Perhaps it's not just girls who want bad boys.
"Secrets" has Artemis getting so jealous of Conner and M'gann's relationship that she needs to leave. What does she do? Go on a Superhero date with Zatanna.
Queen Bee can control men... and some women. Also, her threat to M'gann at the end of "Image" has them get really close...
Just as in the comics Conner Kent is revealed to be the product of both Superman's DNA and Lex Luthor's, meaning he is the child of Superman and Luthor!
Listen to the way Nightwing says "Kaldur" in "Alienated." It's... anguished.
Superboy dragging Blue Beetle while mentioning "personal time".
Their entire segment in the episode could be seen as a 'date', with additional fuel supplemented by Superboy's reactions to Blue Beetle's well-being throughout the mission. (Cradling scene, anyone?) In fact, when Blue Beetle acted as translator for the elemental husk, describing the pain and sorrow it felt, Superboy looks directly at Blue Beetle saying he could reciprocate, shaking himself out of it a second later when he realized what he was doing. With context, you know Conner means his clone issues and/or recent breakup. Without context however...
Icicle Jr thinks Psimon has a 'pretty brain'.
Issue 18 of the tie comic has a panel where the Brain looks like he is stroking Mallah's cheek while saying not all apes could be perfect like him.
Lex Luthor wants to give the original Roy Harpersatisfaction
Impulse really wants to hang out with Blue Beetle, going so far as to randomly arrive at his door and show off. Not to mention running to find him immediately, and hugging/holding Jaime
Their Ho Yay has only since intensified since Before The Dawn, when Impulse reveals that his main reason for going back in time was to save Blue Beetle from being controlled by the Reach (also to save the Flash's life).
And as of True Colors, Impulse is insisting they go on missions together and staying with Blue Beetle during surgery.
Bart: Hey, if Blue's going, I'm going.
Bart fuels the fire once more in "Intervention", from his constant insistence to go rescue Blue Beetle, to his trying to get Blue's attention after he has been freed. Bonus points for that disappointed look when the first thing Jaime does once having control of his body back is to hug Zatanna (out of thanks).
Queen Bee has the ability to control most men so the first mission to Bialya this season was made of all girls. In this episode, the main squad to capture and transport Blue Beetle to Bialya is made of 3 girls and Impulse...
Kaldur bonded easily with Conner and Clone Roy, as all three saw themselves as outsiders.
The very first episode of the show is Aqualad freeing Conner. Many episodes later he always reassures him that he shouldn't be hard on himself.
Aqualad and Red Arrow teamed up many times and each had each other's back.
Red Arrow: Tell me who broke your heart.
Aqualad: Tula: the girl I loved chose my best friend, Garth over me. While, my best friend on the surface world aims an arrow at my chest.
The only one Tye contacts when he's about to run away is Jaime; on it's own, that just looks like good friends. But combined with Jaime spending the entire day looking for Tye, Jaime's excitement at seeing Tye causing him to nearly blow his secret ID, and to top it all off Tye referring to Jaime as 'my man', well...
Bart and Eduardo had some interesting interactions during "Illusion of Control"
At the start, Bart hugs his friends at superspeed including Ed. When you slow down, it almost looks like he's giving Ed a peck on the cheek.
When in a bumper car together, while the others (sans Virgil) are in couples, Ed soothes Bart's frustration of how slow he finds the cars.
Bart: Ugh-oh, this car moves so slow! Will someone please explain why this is even slightly crash?
Ed: My friend, sit back, relax and watch me terrorize the other drivers.
Bart: Woah now. That does put a new spin on things. Drive on, amigo.
Bart got Ed some cotton candy, which he accidentally ate on the way from the booth.
The Running Gag in the episode is Virgil being Alone Among the Couples, and he describes himself as a seventh wheel at one point. The couples present are Jaime and Traci, Gar and Perdita, and Bart and Ed.