It's a quick one, but in "Bad Company", Eliza climbs up and saves Donnie from the top of the tower of stuff the marsupials built to knock down.
Come to think of it, almost any Eliza/Donnie-centric episode is this. She rarely gets annoyed or exasperated with him and the two seem closer with each other than either is with Debbie.
An episode had Nigel delirious from a stonefish sting waiting for Eliza to return with antitoxin. In his delirium, he mistakes a passing catlike creature for his wife, picks it up and tells it how much he loves it and the children — then kisses it. Supposed to be funny, but it becomes more of an "Aaawww..." moment when you realize that he knows these could be his last moments and his thoughts turn to her.
In "The Origin of Donnie," after learning the whole truth about him, each of the Thornberrys talks to Donnie — seeming like an overall "welcome to the family" speech. There is also Donnie's drawing shown during the TV-Movie. It turns out that his crude drawing is actually of his parents, showing that despite his wild boy tendencies, he still remembers them.
What about the official acceptance? Nigel and Marianne are so overcome with emotion that they can't say more than one word. Debbie then takes up the speech by saying in her normal tone "What they're TRYING to say is that out of all the jungle boys we could've found..." She then bursts into tears and walks off. Then to cap it off, Eliza walks up to the confused Donnie and gently says one sentence: "We're glad we found you."
Grandma Sophie is also included and shown that while she has always been accepting of Donnie, though sometimes put off by his wild boy tendencies, she tells Donnie that she's his new grandmother right before bursting into tears of joy like the rest of the family.
When Marianne sees a photo of Donny's parents and realizes that she and Nigel met them before either couple had children. They even give Donnie the middle name "Michael", the first name of his birth father.
In the movie, Eliza gives up her powers to save her sister.
While in the boarding school in London, Eliza manages to fit in with a group of girls, who take interest in hearing about her interactions with wild animals.
Said girls are also happy to help in any way they can to save Tally from the poachers.
Debbie giving Eliza a pep talk after her powers disappear.
Debbie gets a surprising amount of these in the movie; particularly, her friendship with Boko and a scene where she reads "Jack and the Beanstalk" to Donnie.
Darwin sticking by Eliza's side even after Eliza loses her ability to communicate with him, especially since the last thing she said to him in his language was screaming at him to be quiet.
The ending. After Eliza gets her powers back, Debbie becomes her Secret Keeper and Tally's returned to his parents, the Thornberrys all have a Dance Party Ending, instigated by (who else) Donnie. As joyful wackiness occurs all around him Nigel turns to the camera and narrates "The furless primates behind me are part of an untamed subspecies, known as the Thornberrys!" before beckoning Marianne to dance with him, which she accepts.
In "Look Who's Squawking," Eliza puts Darwin in charge of a penguin egg while she runs off to assist the parents. She comes back to find him singing gently to it and very much opposed to giving it up, even breaking down in tears when he watches it hatch. At the end of the episode, the parents name the chick Darwina.
The episode "Forget Me Not", where Eliza befriends Rebecca, an elephant that her father rescued from poachers when he was younger.
Nigel keeping Eliza from freezing to death through sheer badassery.
From "Flight of the Donnie", the mother condor reuniting with her hatchling.
Mama Condor: Who's mommy's little BONE PICKER? Baby Condor: I am!
In "Operation Valentine", it is Donnie who runs across the Australian outback by himself (with an eagle chasing him) to find Nigel and lead him to Eliza, who is suffering from acute appendicitis.