In Season 1 most people consider the fact that Saito preferred Louise before she was under the influence of the Love Potion as an Idiot Ball moment, but think about it, he actually loves her the way she is.
Again in Season 1, Saito comes back to save the day, despite having no obligation to help fight.
Season 2 episode 4, when Saito confesses to Louise and they make out for several minutes in a boat.
The light novel's Volume 11's epilogue. Louise and Saito, after all the troubles they went through, reconcile and kiss; notable because of Louise (sort of) admitting her feelings for Saito directly to him, and him not screwing up his time alone with her, unlike in previous occasions.
Volume 13's Chapter 8. Louise asks Saito out for a date. Thinking it's a trap set up by Louise, Saito is suspicious of her behavior, but he agrees. They spend all day together, Saito noticing Louise's not so frequent smile, even kissing twice. Doubles as a Tear Jerker, as Louise, being told of the World Door to return Saito to his world, decided to spend her time together with him, thinking that day might be their last being together.
Volume 14's Chapter 9 and Epilogue. After Louise gets her memories about Saito erased by Tiffania due to him returning to his world (actually being sent 6000 years into the past by Julio) and her not wanting to suffer from his absence, Saito comes back to save her and their friends from Myoznitnirn's golems. After a while, Louise regains her memories due to Saito kissing her, and later they, alongside their friends, destroy the remaining golems. Later on, as everyone celebrates victory, Louise and Saito talk about his decision of coming back and their memories together. Turns into a Funny Moment as Louise sees a memory of Saito making fun of her while she was in a trance due to being under the effects of a crappy love potion, although he didn't know that fact.
Volume 18's Chapter 1. After Louise's return from Saint Margarita (where she fled to due to seeing Saito and Henrietta kiss) to save Saito from Jack of the Elemental Siblings, Louise and Saito reconcile after a long but heartfelt discussion.
Chapter 9 from the same volume. Eleonore, Louise's eldest sister, pays Louise and Saito a visit to their home. After Eleonore questions Louise's decision to live with Saito, Louise stands before her and says she'd rather lose her title as a noble than being separated from him. Eleonore was reluctant about Louise's decision but later accepts it. As Louise and Saito prepare the guest room for Eleonore, who ordered them to sleep in separate beds due to them not being married yet, Louise asks Saito where will he sleep. He replies he'll sleep on the couch, but she shows concern for his comfort, a sharp contrast to when they first met, where she ordered him to sleep on the floor, a fact Saito lampshades while receiving an apology from Louise. Later they spend a little time alone together on the couch.
In Season 4, when an Ancient Dragon goes after Void mages, the place to fight it is decided to be the Academy of Magic. All students are evacuated... except for Louise's classmates — who decide to stay and fight the Eldritch Abomination alongside Louise!
Also, after Kirche learns of Tabitha's dark past and sees her haunted by nightmares in her sleep, she decides to lie beside Tabitha and embrace her, telling her everything will be alright.
Season 4 takes the cake. Saito proposes to Louise in front of everyone. Louise doesn't even try to hide her happinness and accepts it wholeheartedly. Then they get married. FOR REAL. Possibly in the same chapel where they got married in Season 2. With everyone (meaning the girls + their teachers + the royals + the elves + LOUISE'S FAMILY) attending and genuinely happy for the two lovebirds. Playing to the tune of 'I SAY YES (Wedding Version)' from Season 2's final episode. If that's not heartwarming enough, then let's go for the epilogue. Louise and Saito arrive at their newly rebuilt manor in Des Ornieres. Then they get off, Louise uses World Door, and she and Saito go to Japan. Louise experiences our world for the first time, including riding the bullet trains, sightseeing, and eating crepes. They finally reach Saito's house, where they push the doorbell hand-in-hand, their wedding rings glistening on their left hands' ring fingers and Saito's Gandalr runes still visible. Louise doesn't look annoyed, or angry, and she's really enjoying their precious time together. All this to the tune of Louise's happiest (or at least the only one where she doesn't snap at Saito) rendition of 'Kiss Shite Agenai'. All together now, D'AWWWWWWWWWWWWW~...
Meta: The author passed away with the hopes of finishing the novel series at 22 volumes. Four years after his passing, he gets his wish; the series continued to completion due to his team's hard work.