In CLANNAD there is a misunderstanding between two girls, when Ryou thinks Nagisa wants to confess her love to her. Nagisa only wants help with her drama club, but Ryou's positive response comes suspiciously early ("Yes! HUH?") and the sudden yuri imagery also doesn't help. The guys who set this up get their comeuppance when Ryou's sister Kyou rushes in and demonstrates her double head-lock on them.
The relationship between Sunohara and Tomoya is often cracked on by Tomoya himself, especially seen in the second-to-final episode before the OVA.
Also, Kappei with both Tomoya and Sunohara, get both an Unsettling Genderreveal. Sunohara, in denial, still pursues what Tomoya calls "unrequited love."
In minor character examples, Rie and Sugisaka, the two girls from the chorus club, are almost never seen without each other. They hold hands in the second season ED, and in the epilogue, they're seen living together.