Deloris and the Reverend Mother at the end of the first film. Yeah. That scene.
Don't forget the scene where she defends Deloris as a true nun and "a model of generosity, virtue, and love."
"Out of bed, you Daisy head." That whole scene with Mary Robert, actually.
The scene after the first choir practice, when Deloris is lying in bed listening to all the nuns practicing their chords, and it ends with Mary Robert hitting a perfect, beautiful note. The smile on Deloris's face really sells it.
The look of pure joy on Mary Robert's face after her first solo during "Hail Holy Queen."
Which leads to another heartwarming moment when you can tell she has immense confidence in her voice during her other solos. (And then immediately afterward she's blushing and trying to cover her face, like 'What did I just do?')
Well, heck, every scene with Mary Robert is Heartwarming.
Also, look closely after Mary Robert's solo in "Hail Holy Queen." As she turns in thrilled excitement, Sister Mary Lazarus—a Grumpy Bear to the extreme—has a huge smile on her face and congratulates her on a job well done.
In universe, how the nuns feel after going out into the community after being cloistered for so long. They long to do good works and now they finally get the chance to revitalize their run-down neighborhood.
It also works as an audience example, too. We see the nuns going into the community; rather than proselytizing, they strike up friendly conversations, run a soup kitchen and garden market for the homeless, create beautiful artwork, and even fashion a playground for poor youth out of junk. Deloris even leads Sisters Mary Patrick and Robert in meeting some teenagers, and the two groups create a genuinely friendly bond over jump roping and dancing. Even atheist YouTube users comment that the spirit of the scene—that of religion doing small, good deeds with compassion and producing tangible results for those in need—is a powerful, positive one.
After the kidnapping scene happens, the rest of the nuns express confusion as to why anyone would kidnap a nun. Reverend Mother decides to come clean about who Sister Mary Clarence really is: she's a lounge singer from Reno named Deloris who was placed in the Witness Protection Program after witnessing a murder. While the nuns are obviously stunned to hear this (as well a little upset about being lied to), Sister Mary Roberts declares that she doesn't care who Deloris really—actual nun or not, she saved the church and the choir, and that's enough to make her a loyal friend and a good person. Sister Mary Patrick supports this statement, and Sister Mary Lazarus then states that they shouldn't leave saving Deloris up to the feds if they can it. The rest of the nuns, including Reverend Mother, agree with this and they immediately set out to Reno.
At one point, Sisters Mary Robert, Patrick, and Lazarus sneak Deloris down to the kitchen at midnight and produce some "contraband" for a secret snack...tubs of ice cream. Even Mary Lazarus, who first calls it a "wicked indulgence," wants to know where the butter pecan is. It's small and even silly, but seeing the nuns so happy and thankful to Deloris that they're willing to bend their vows is adorable.
During the first rehearsal scene, Deloris takes over the choir. At first, she's reluctant, but as she gradually gets into the role, she rearranges the room and demonstrates her strong knowledge of music. She even gets into the spirit (literally!) of the convent by pointing out that singing is a form of praise and worship. It's the first time we see her genuinely beginning to enjoy herself and relax, and makes it clear that there's a heart of gold beneath her snark.
From the same scene: Mary Lazarus was the former choirmistress, and is upset when Deloris takes over her part. Rather than being sarcastic or dismissive, Deloris finds a way to integrate Mary Lazarus into the process, asking her for advice and allowing her to make the rehearsal schedule. Mary Lazarus is thrilled (not that she'd ever admit it), and again, it shows the kind side that the convent reveals in Deloris.