Muhyo and Roji. A two-page spread devoted to their reunion surrounded by flowers? What's more, at the end of the series, Page says that "a golden thread" binds them, and while the twins make fun of him for his poor choice of imagery (gold is not a very sturdy metal), there is no denying that they have a bond.
Muhyo's relationship with Enchu is, in some ways, reminiscent of Naruto's similar relationship with Sasuke. In both cases, the latter turns traitor, and the former becomes determined to bring him back at any cost, up to and including dying together. Enchu's similarly obsessed with making Muhyo suffer.
Yoichi and Enchu. Despite being a pervert and a womanizer, the majority of Yoichi's time goes into investigating Enchu and tracking him down.
Ebisu and Goryo. Some moments cross the line from simple familiarity between Executor and assistant and become completely ridiculous.
Les Yay
From the first chapter, Rie and Taeko had a Pseudo-Romantic Friendship while the latter was alive, as each other's Only Friend. They didn't even mind that other people found their closeness a bit gross, almost like a lesbian couple dealing with homophobic classmates. Taeko's reaction when Rie started hanging out with the volleyball team comes off as vaguely like a jilted ex-girlfriend.
Biko and Rio. Biko adores Rio as her teacher, who's rather affectionate when the two meet again. Biko offers to be there for Rio in the same way that Rio was there for her mother, and Rio, despite having already turned evil, is deeply touched by the gesture.
Imai and Busujima are long-time friends, with Busujima confident that Imai can survive any situation she's thrown in, but being disappointed in Imai's flat chest. When Imai catches Busujima smuggling an elixir that she's using recklessly, she pulls the vial from between Busujima's breasts.
