Lex's obsession with finding Brainiac in the final season of Justice League Unlimited is pretty intense. To be fair there's probably little other way to play the search for someone you once shared a body with, but still. Of course, it seems even more slashy when you start hearing Lex's dialogue ("We can finally be together again!"). Then there's the fact that Tala, his lover, betrays him because she's sick of him always pining after Brainiac. Nope, nothing suspect about that at all. Not to mention the attempted resurrection in "Alive," which includes a close-up of Lex's ecstatic face while he exclaims "Brainiac... I'm coming!"
At the beginning of the three-part story "The Savage Time", normal Batman was replaced by freedom fighter Batman due to Vandal Savage changing history. After setting everything right, the Justice League returned to their original timeline. When normal Batman shows up, Superman runs over and hugs him◊. The rest of the Justice League smile sympathetically.
Justice League had more than its fair share of Superman/Batman Ho Yay, the pinnacle of which occurred in the episode "Hereafter". Superman is vaporized in the first act, and Batman's response is to carry around a scrap of his cape, finger it absently while reviewing a tape of Supes' death ad infinitum, and maintain to anyone who'll listen that he's not quite dead. Of course, this being Batman, he'sright, but League members still manage to call him out on his stoic bullshit. And then there's this speech:
Batman: I've got some things to say. I should have said them when you were here, but... despite our differences, I have nothing but respect for you. I hope you knew - know that. You showed me that justice doesn't always have to come from the darkness. I'll miss - " [explosion in the distance] What did you always call it, Clark? The never-ending battle?
In the Justice League episode "Maid of Honor", Wonder Woman and Princess Audrey have a... very close relationship after a night of partying. Considering that Diana is an Amazon hailing from a society with no men whatsoever and Audrey just radiates that "depraved aristocrat" vibe, one might wonder what exactly went on that night.
Especially prevalent in that afterward Audrey started to treat Diana like a clingy, jealous ex because she was trying to stop her marriage with Vandal Savage.
Also note how earlier in the episode, Audrey even says "I'm a world class party girl, I intend to go out with a bang. Several, if it can be arranged" then winks at WW. Then later she's flirting with 4 "hot guy" types, offers 2 of them to WW, then suggests they both "go to the VIP room"
Batman going from dismissal to grudging respect for Flash would be fine on its own, but there's the episode "A Better World", and JusticeLord!Batman repeatedly apologizing to Flash for taking on the League, leaping down the stairs when he believes Flash is dying, and not checking any kind of security before releasing Flash's bonds.
Batman [to Flash]: I think he likes you.
Huntress and Black Canary have some pretty strong subtext in Grudge Match. Question (aka Huntress' boyfriend) calls Huntress out on essentially stalking Black Canary, a woman who she's not even supposed to like, and she defends herself in embarrassment while she watches Black Canary in her room. When they give in to temptation and agree to have a fight at the end, Black Canary takes off her jacket and Huntress takes off her belt.
Of course, the entire episode was known for its Les Yay subtext - as is every other Black Canary story these days.
In Starcrossed, Hro Talak's lieutenant Kragger seizes every opportunity he can to cock-block Hro and Shayera, who are engaged. Towards the end, he's actually smiling as he does so. When J'onn looks into his mind, we see statues of Shayera, Hro and Kragger. The Shayera statue is broken and crumbled, and the Kragger statue has replaced it by Hro's side.
When the Thanagarians return in Justice League Unlimited and Kragger is basically a vegetable in a robot suit, almost all of his dialogue is reinforcing the Ho Yay between him and Talak. "You took Commander Talak from us!". It wasn't her costing his home planet the war and dooming it's survivors to enslavement that made him really upset, it was her "taking Talak from us".
According to Bruce Timm, "[Kragger] plays Hro Talak's right-hand man who probably is a little bit more than that — at least in his own mind, which is pretty obvious when J'onn gets in here, we see the two big statues with the crushed statue of Hawkgirl laying at their feet. A little bit of symbolism there, which amazingly went over a lot of people's head."
The camera slowly zooms in on Kragger's face as Vixen speaks: "Shayera and I, we...want the same man." And then Kragger's willing to believe Vixen's offer of betrayal completely.
There was something between a serious bromance and this trope going on between the Shining Knight and Vigilante. They were only ever in episodes and fight scenes together (except for Vig in Hunter's Moon, anyways).
Justice League episode "The Balance", contains a lot of Wonder Woman and Hawkgirl lesbian subtext.
In Fury, Tsukuri's loyalty to Aresia boarders on Les Yay. They're both trying to eradicate men from the planet. Not to mention one particular scene where Tsukuri refuses to leave Aresia behind, even when it was just the plan.