My favorite "arc" is when Calvin finds the dying raccoon, takes him in to try and save him, the raccoon dying, and realizing that even though he's sad that the he died, he's still glad to have met him while he had the chance.
Calvin coming to terms with death, and realizing that even though fatalism is basically the only inevitable outcome in the long-term, it's important to enjoy life now and enjoy the current relationships we have is enough to get me teary-eyed (even to this day), and has greatly shaped my outlook on life, since I read it when I was really young.
It's a great comic, and despite centering on a child, it does a really good job at using that kind of innocence as a means to make a commentary. Watterson resisted the urge to talk about politics or pop-culture, and instead focus on people, and as a result the comic will always be timeless to me