Leeron openly flirts with Kamina, Simon, Viral, and Rossiu.
For a more subtle example, Rossiubreaks down crying after he orders Simon's execution, and Simon drills through time and space to stop Rossiu killing himself, delivering a Get a Hold of Yourself, Man! punch that would make even Kamina jealous.
For a less subtle example, there's Simon and Viral's fistfight, where both of them are wearing nothing but suspiciously tiny towels.
None of this however can compete with Simon and his "aniki" Kamina. The story of them caught in an earthquake together, in which they both describe the other as an indomitable source of strength and the inspiration for the person they are today, possesses more romantic undertones than the entire rest of the series. Check out their hug in the first episode where Kamina cradles Simon's head to his chest, and in second episode where Simon falls asleep in Kamina's arms. Then, in one episode (after Kamina's death, that is) Simon is shown spending his time making statues of Kamina and nearly filling up his room with them.
Viral dreams about Kamina in drag  during the short, "Viral's Sweet Dream."
Leeron: "Just stick it in! Give it a big, manly twist!" Also, in one episode where Dai-Gurren is sinking, Simon pushes it back out of the water... by pushing it with his drill. Cut to Leeron inside the Dai-Gurren, who feels the impact in his ass.
At one point in episode 6, Simon leaps over Leeron, but his crotch doesn't quite clear him and Leeron gets smacked in the face by Simon's junk. Leeron responds simply by saying "So warm."
Kamina: Combining is where two fighting spirits collide! It's where a man's spirit is ablaze!
Simon: You made it work out well. As expected from you, Leeron.
Leeron: I'm not satisfied with words of praise, I want your burning heart!
Viral: Can I kill him?
Simon: Not now.
Then there's Nia and Yoko's haircutting scene at the end of episode 12. The manga adaptation of the scene makes it more blatant.
Also from episode 6: Gimmy sticking his finger up Simon's butt in the hot springs when ordered by Kamina to "find a hole" (so he can peek at the girls bathing on the other side) which sends Simon flying into the air so that he can see the nude girls for a split second.
Which prompts Kamina to smack his own butt repeatedly while yelling "COME ON, GIMMY! COME POKE ME IN THE BUTT!!!"
As an overall theme, a good chunk of Ho Yay lies the series' understandable-in-context obsession withdrills. With the show's cast being vastly comprised of manly, Hot-Blooded males alongside young females like Yoko and Kinon who are implied to be of the Yaoi Fangirl/Fujoshi persuasion, if the show's message is taken even slightly out of context, all the drill talk seems to deteriorate into one big euphemism. With the filthy place this show has a knack for putting certain viewers' minds in... it's safe to say that Freud was definitely right.