Gertrude the duck from the 1959 film and all the A Boy and His X moments she inspires.
The most heartwarming moment of the 1959 version is the fact that everybody wanted Professor Oliver to take the bow for his amazing discoveries. But he instead gracefuly refuses, saying that since he can't prove any of it he shouldn't brag about it.
In the book, there is a moment when the trio are dying from dehydration. They're pretty much crawling down the tunnels at this point, and Axel realizes they are going to die. Then, just as they have all collapsed and he is starting to drift off, the professer gives him the very last dregs of the water he had been saving just for Axel, and apologizes for getting him killed. They revert back to their previous relationship after surviving, but it's probably the sweetest scene in the book.
The moment in the book when the trio emerges safely on Stromboli in the sunshine and looks around at the beautiful view is incredibly uplifting. The detailed description of the view really conveys how stunning it must have appeared to the characters after months underground and just escaping mortal peril.