For reference; most boys Calvin's age would poke a dead bird with a stick. Calvin waxes philosophical about it instead.
The one where Calvin and Hobbes figure out that they can play together all night by dreaming about each other, then go to bed saying they'll see each other soon. Seems more like a Heartwarming Moment, until the 10th Anniversary compilation where Bill Watterson revealed that he wrote that strip after the death of his cat Sprite, who was the major inspiration for Hobbes' look and personality. "We can always meet again in dreams."
As sweet as a plum, as lovely as dawn, rolling its tongue over its gums:
My tiger and me, as happy as could be, sat out on the porch as the whole of the sky clouds quietly over.
And it starts to cry, softly, on my shoulder.
We don't want to grow up, but we have to grow up. As sad as I am, I do understand. I do understand, it just makes me sad.
My tiger, my heart — We're growing apart. We're trying to be friends, but it's hard sometimes to be friends with something that eats butterflies and pencil sharpeners, and I think it would be happier being free...
My tiger, my friend, my little godsend. I know someday we'll be happy again.
The family returning home from a trip (on which Hobbes had been left behind at home by mistake) and discovering their house had been broken into. Dad muses how he doesn't feel safe in his own home anymore.
"A man's home is his castle, but it shouldn't have to be a fortress."
Meanwhile, Calvin is practically in hysterics trying to find Hobbes because he thinks his best friend has been tigernapped. (Thankfully, he was not.)
"Mom says Hobbes wouldn't have been stolen because he's not valuable. (sniff) Well, I think he's valuable."
Calvin's mom's take on the break in.
"This is something that you always figure will happen to someone else. Unfortunately, we're all 'someone else' to someone else."
The baseball story arc. Calvin signs up for a baseball team, but close to the end, Calvin messes up by accident and makes his team lose. All of the other players cruelly insult Calvin, for something that wasn't even his fault! (One of them even asks if he can hit Calvin with the bat.) The kicker? At the end, Calvin asks the coach if he can sign off and the coach says, "Okay, quitter! Goodbye." Thankfully, Hobbes has a better idea when Calvin gets home.
There's also the story arc when Calvin has to tell his father that he broke his binoculars, and Dad flies into a tirade lasting for almost an entire strip. At the end of it, a tearful Calvin looks up at the man and says: "I have an idea. Let's pretend I already feel horrible about all this and that you don't need to rub it in anymore."
What's worse is that throughout the story up to that point, Calvin is genuinely worried about how angry his father will be, and it almost makes the reader wonder if his fear is just making things seem worse in his head. It's not.
Many of the heartwarming scenes between Hobbes and Calvin become outright devastating if you agree with the interpretation that Hobbes is only alive in Calvin's imagination, and that that's all he has.
Ka-ZAM!◊ Watterson comments in the tenth anniversary book that "imagination is not always appreciated."