One Sunday strip features Calvin getting ready for a day at school one rainy morning. That's it. No dialogue, no Imagine Spot, no wacky hijinks...and the last two strips feature Calvin staring at the clock, bored and miserable, while Hobbes stares out the window in the rain, waiting for Calvin to come home. Of the three characters (Calvin, Hobbes, and Calvin's Mom) nobody smiles once.
One of the earliest story arcs of the strips deals with Hobbes having been stolen from Calvin by a dog. Calvin's desperation as he searches for his best friend really hits home, especially to those readers who had beloved toys lost and stolen as kids. It's also one of the first times in the strip Watterson received fan mail from readers genuinely concerned about Hobbes' wellbeing.
Rosalyn and Calvin never get along, due to Rosalyn starting her babysitter stint by locking up Calvin in the garage and then in his room. Calvin then retaliates, and they never really find common ground... until he teaches her how to play Calvinball.
The storyline where Calvin and Hobbes find an injured baby raccoon and rally the family together to try to save its life. They don't succeed.
Calvin's dad has to break the news to him. He's not happy about it, especially when Calvin starts to sob loudly and says he just can't believe the raccoon is gone.
Dad: At least he died safe and warm. We did everything we could but now he's gone.
Calvin:(sniff) I know. I'm crying because out there he's gone, but he's not gone inside me.
Calvin and Hobbes go to the woods where Dad buried the raccoon. Calvin laments how painful and unfair it all is, and ends up being scared by the concept of death.
Calvin: He was just little! What's the point of putting him here and then taking him back so soon?! It's either mean or arbitrary, and either way I've got the heebie-jeebies.
Crossed with a Heartwarming Moment, the arc ends with Hobbes and Calvin ultimately accepting that death is just simply a part of life and then make a promise that they're not going to leave each other.
Calvin: Mom said death is as natural as birth, and it's all part of the life cycle. She says that we don't understand it, but there are many things we don't understand, and we just have to do the best we can with the knowledge we have. I guess that makes sense... but don't you go anywhere.
Hobbes: Don't worry.
This story has a bit of Reality Subtext to it, as Watterson said it "just wrote itself" when his wife found a dead stray kitten one day.
What makes this one especially heartbreaking is that it's probably the only time we see Calvin genuinely concerned about someone other than himself, and genuinely upset about something real and very sad, not just a variation on "he didn't get his way".
For reference; most boys Calvin's age would poke a dead bird with a stick. Calvin waxes philosophical about it instead.
Another bit of Reality Subtext. The dead bird sketched in the first panel was one that Bill Watterson found outside his home.
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."
"A man's home is his castle, but it shouldn't have to be a fortress."
Later, he talks to his wife about how, during his own childhood, he always trusted his parents to fix everything, and it never crossed his mind that they might not have any idea how...which is the same situation he's in now.
Meanwhile, Calvin is practically in hysterics trying to find Hobbes because he thinks his best friend has been tigernapped. He even tells his mother that "Hobbes is so trusting," especially since Hobbes is established as a misanthrope. (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 due to being bullied by Moe for being the only boy who didn't sign up. However, close to the end, Calvin accidentally catches the ball for the wrong team and makes his team lose. All of the other players cruelly and mean-spiritedly insult Calvin for an understandable mistake, in a way that really hits close to home if you've been bullied yourself. (One of them even asks the coach if he can hit Calvin with the bat.) The kicker? Due to this name-calling, Calvin asks the coach if he can sign off. The coach's response? "Okay, quitter! Goodbye." Thankfully, Hobbes has a better idea when Calvin gets home.
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.
Ka-ZAM!◊ Watterson comments in the tenth anniversary book that "imagination is not always appreciated."
Also, Hobbes shows No Sympathy as Calvin, still sick, lays awake in bed fretting about if he'll go to the hospital or if he's dying. To be fair, Hobbes himself doesn't want to catch Calvin's bug too, but still...
Susie wants to be friends with Calvin, or at least play with the only kid on their neighborhood block. Calvin refuses, due to Susie being a girl. He has made her cry, tossed apples and pine cones at her, and refused to play house her way. While he is sincere at times, like when he thanks her multiple times for finding Hobbes and keeping him safe, Calvin is too mean the rest of the time.
Add the implication from several story arcs that she's a staunch perfectionist who often panics that a failure in first grade could ruin her chances of getting into a good college, and Susie really is prime woobie material.
One that takes a moment to sink in is the Sunday strip that walks Calvin through the various hardships and frustrations of a typical school day. When his mom kisses him goodnight and promises that "tomorrow's another big day!", Calvin's only response is a defeated sigh. Watterson's comment on the strip in the 10th Anniversary book sums it up:
I've never understood people who insist that childhood is an idyllic time.
An earlier strip had the same theme, where Moe punches Calvin and knocks him into the mud for no reason, then leaves laughing, leaving a miserable Calvin to remark, "People who are nostalgic for childhood were obviously never children."
Yet another strip begins with Calvin angrily complaining about having to go to school even though he hates it, only for Dad to tiredly tell him that in that case, he can go to work all day to provide for the family, with the only reward being the griping of a whiny kid. Cut to Calvin standing at the bus stop with a sour look on his face.
Calvin: It's nice to know there's so much to look forward to in life.
In one strip, Calvin asks Dad why grown-ups never play outside, and Dad answers that grownups have to justify "playing outside" by calling it "exercise", rating and scoring it, and doing it whenever they'd rather not.