Heavy amounts of Les Yay are present between Saki and Nodoka. There's Nodoka blushing around Saki, Nodoka constantly thinking about Saki, Nodoka telling Saki about the constellation of two lovers, and the other people noticing it to the point that they state that Saki is a huge source of distraction for Nodoka. Consider how Saki often reciprocates, it's a wonder the two haven't given in and made out. Point in case would be in Episode 10, in which Nodoka consciously snuggles closer to Saki to hug her while they sleep together.
In the final episode of season 1 they very meaningfully exchange charms and walk down the steps from a shrine, with Intertwined Fingers and very triumphant sounding music playing behind them...
Hisa and Mako have a mild one going on too, what with Hisa telling Mako that she, the only other member of the club in Hisa's second year and Mako's first, is the only reason why Hisa never gave up on the Mahjong Club.
Meet Kazekoshi Girls' School's Mahjong club, where every member has a huge crush on their captain, Mihoko. They get jealous of their fellow team members if the captain cheers her on or comforts her with a hug. In the third ending, The Team creates a massive sand sculpture for their captain.
Mihoko has her eyes set on someone else, namely Hisa, who once managed to beat her after she opened her Magical Eye then called her eyes as beautiful after the match. Mihoko never forgot about her and wanted to meet her again, though sadly, Hisa dropped out of the tournament scene afterwards and had apparently forgotten all about her, until she opened her right eye again in the individuals. Since then, the two are often seen together, and Mihoko tends to open her right eye when around Hisa. (And blush and lock up when Hisa complements her.) Ho Yay enthusiasts will devour the fact that in the second episode of Zankoku-hen, before the others have woken up, Hisa is seen standing in front of Kiyosumi's closet and Mihoko's uniform is hanging with theirs.
From Ryuumonbuchi High School we have Touka and her maids.
Tsuruga Academy's main couple of Yumi/Momoko, who was last in for the Les Yay department but is definitely not the least. Yumi storming into Momo's classroom and screaming "I want you!" for their first meeting? Momo being so touched, she not only appears before Yumi, but is now fine with her non-existence as long as her one special person can see her? The two of them are shown going out on dates afterwards. The usually Shrinking Violet Momoko glomping Yumi in public while screaming "I love you, sempai!" and the usually stoic Yumi blurting out an embarassed "Not here!"? My goodness, if their relationship still isn't considered canon, it should be!
From Achiga-Hen, there's Toki and Ryuuka, who have been friends since middle school and are very close. Ryuuka often lets Toki lay her head on her lap, and becomes especially anguished when Toki overexerts herself in a bid to take Teru, the champion, down a peg.
From Shindouji, there's Mairu and Himeko, who have been friends since middle school. Their Combination Attack not only looks as though Mairu is engaging in bondage, but also is said to run off The Power of Friendship.
. Or a less convenient 10-minute package