When Ian is being baptized into the Greek Orthodox Church.
Toula: He's gonna look at me and say "you're so not worth this!"
Nick:Yes you are.note Nick spends most of the movie up until this point behaving very immaturely, so to hear this from him is a sign of Hidden Depths
At the wedding, when Gus hands over the wedding gift from him and Maria, and Toula opens it to reveal that they have bought Ian and Toula a house. It shows how much Gus has grown, and his acceptance not only of Ian, but of Toula's choice.
Toula and her grandmother really getting to connect the night before her wedding is a beautiful scene.
Toula revealing herself as "frump girl" from the Greek Cafe, Ian only replies:
Ian: I don't remember "frump girl" but I remember you.
Toula, after Ian compliments her in an almost-offhand, "it's so obvious" fashion:
Toula: Did you say I'm beautiful?
Harriet and Rodney dancing with the Portokaloses at the wedding reception. It seems the dry toast has some flavour after all.
Gus's little speech at the Reception counts when you think about it closely. In the scene prior to the wedding, he openly refers to the Millers as being "dry toast" (that is, boring) but then at the reception has realised "hey, we're all different but in the end, we're all fruit." (In other words, it's OK for us to be different because we're still human).
From the sequel:
Nick observes Angelo and his business partner and when they talk about how funny Toula is acting, Nick states that she'll tell him because "Why would you hide things from your family?" with a wink. Hearing this, Aunt Voula finally asks him:
Voula: "Is he your partner, or your partner?"
Angelo: "He's. . .both."
Voula: "I know."
(they embrace, and Angelo's relief at his mother's acceptance of his lifestyle is palpable)
Paired with "Funny", when Angelo's mother is formally introduced to his boyfriend, she begins regaling him in the same overbearing manner that we've seen all the parents display, driving home the fact that she will not be treating him or their relationship any different from the heterosexual ones.