Hinata and Otonashi. About once in every two episodes Hinata will say something (such as "I quite like you" or "I need you!") that makes him sound like he has a crush on Otonashi. Cue Otonashi asking "Are you..." with a troubled look and an Aside Glance, and Hinata hurriedly cutting him off. "It's not like that!". It's pretty much a Running Gag.
And on Otonashi's side, running to Hinata when Hinata was about to disappear from their lives desperately thinking, "HINATA! I...I don't want you to leave!!" (or something along those lines) was pretty dripping with Ho Yay.
It's taken even further in a few of the drama CDs, with Yuri in one of their acting sprees demanding that they reenact the scene in the second episode—-where, when in peril, Otonashi has to figure out the finesse of how not to accidentally grope Yuri while climbing above her and Hinata—from a HinaOto perspective on both sides (because of the pairing's immense popularity at the time on Pixiv).
As of Episode 6, Otonashi and Naoi.
Naoi: So then... You'll acknowledge... My existence?
Otonashi: Who else is there? You're the one I'm embracing. There's no one but you. There's only you.
The embracing mentioned above is featured in the picture.
Episode 11 has Hinata and Naoi trying to out Ho Yay each other to help Otonashi.
Towards the end there's some Les Yay between Yuri and Kanade.
Episode 12. The part leading up to the reveal about the source of love can come off as this. Yuri thinks about taking all that power and says, "I can't do that to Kanade anymore. After all, I only made it this far because I..." and then all the screens light up with red hearts. Course, then it turns out she was thinking about the whole SSS.
Hisako with Iwasawa in chapter 14 and the omake in the Heaven's Door manga, with Iwasawa hugging Hisako, saying things like "I need you" (which Hisako reciprocates) while poised over her, testing Hisako's breasts' sensitivity, accidentally ending up with a nude Hisako poised over her...
Continued in chapter 26. Yuri even orders them to stop all that lovey-dovey stuff.
Remember what T.K. said in episode 12 when he saw Matsushita all slim and fit? "TastyCandy."