In the pilot episode alone, Aqualad and Superboy have no less than five subtly flirty scenes.
The beginning of "Denial", where they sparred with Superboy's shirt off.
The entirety of "Targets", between Aqualad and Red Arrow.
Two examples from the 13th issue of the comic. Robin teases Kid Flash by calling him "Freshness" and then trying to Spot the Imposter by asking both KF's what his (Robin) middle name is (They were both Clayface).
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.
The same scene has Wally loudly protesting Artemis being on the team in place of Red Arrow, very upset that the team is getting a hot blonde in a navel-baring outfit instead of Roy. He makes it clear he'd rather have Roy than some girl. A girl who he actually finds beautiful as revealed in the memory loss episode "Bereft". Wally, an unabashed flirt who really loves the ladies.
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.
M'gann is so devastated and traumatized by Artemis' simulated death that her subconscious—despite her conscious mind knowing it wasn't real—hijacks everyone's brains and sends the simulation spiraling out of control.
Happens again in season 2 when M'Gann thinks Artemis has been killed by the now supposedly evil Aqualad and she mind rapes him in retaliation - only to discover that he was actually a mole and Artemis is alive and well and being a mole as well. She didn't take that revelation very well.
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...
"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!
In "Auld Acquaintance", Red Arrow asks Aqualad to tell him "who broke [his] heart" to prove he's not being mind-controlled. Aqualad's answer? Tula... and Red Arrow himself.
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. Possibly doubles as Getting Crap Past the Radar because they are boyfriends in the comics.
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...
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...