From the first episode: Rick tells Morty to keep shooting the Galactic Federation soldiers, yelling "You have no idea what prison is like here!" It seems like a throwaway gag, but as of "Wedding Squanchers", Rick has been thrown into Maximum Security of said prison, and it's revealed to be a place where inmates are kept affixed, immobile, to giant X's. Presumably forever.
Also from the first episode, the first thing we see Rick doing is preparing to blow up all life on Earth. Just drunk Rick being drunk Rick right? Given how this was Prime's home world-as in the man who destroyed all Rick held dear with a bomb-the idea that a drunk Rick would think it right to destroy his world with a bomb isn't out of the question.
One of the first lines Rick says to Beth is "This was a good breakfast Beth, you really made the crap out of those eggs. I wish your mother was here to eat them." At the time this was just Rick either manipulating Beth or actually being genuine (with Rick, it can be hard to tell), given how this was one of the only times where Rick talked about Beth's mom. Then "Solaricks" revealed that the Beth he was talking to was Beth Prime; the one from the man he had been hunting for decades because he killed his wife and daughter. Whether Rick was secretly venting his hatred for Prime with the comment, or was genuinely sorry that this Beth lost her mother in addition to having such a horrible man as a father, the statement does not have happy connotations.
In "Meeseeks And Destroy", Rick sarcastically tells Morty that they will be easily raped in giant prison because, when they drop the soap, it'll land on them and crush their spines. Mr. Jellybean's attempt to rape Morty minutes later is not quite so funny.
In a more meta sense, the already distressing scene gets even worse come 2023, when Justin Roiland was accused of, among other things, sending inappropriate DMs to underage fans, leading to his dismissal.
Relatedly, the plot of "Rick Potion No. 9" falls into this, with Morty wanting Rick to make a Love Potion, which not only does Rickcall him out on it, but he even outright calls it a "roofie."
Anytime Rick says "Wubba Lubba Dub Dub" becomes this once Birdperson reveals what it means in his language: "I'm in great pain, please help me".
Every interaction between Tammy and Birdperson when it's revealed that she was fooling him into falling for her so that she could spring a trap on him and all of his anti-government friends at their wedding.
Rick's indignant attitude towards being invited to their wedding becomes more sympathetic and understandable when later seasons reveal he loved Birdperson and was rejected, as Birdperson felt they should be Just Friends. Imagine how you'd feel if your ex who dumped you invited you to their wedding.
Rick takes offense in "The ABC's of Beth" when Beth says that Froopy Land was a dumb name for the secret world she thought that Tommy had disappeared into when she was a kid. He tells her that he put a lot of effort into making it for her so that she would never get hurt and would remain safe. "Rickmurai Jack" confirms that our Rick lost his Beth when she was a child, meaning that knowing that multiple Ricks built Froopy Land as a safeguard to ensure their daughters would reach adulthood.
Seeing the Vindicators getting killed off in their "third" big adventure can sting a bit if you've had to see your favorite character die in Avengers: Infinity War. Ironically, the founding members all survived in that one.
Seeing the Narnia dimension from episode "Mort Dinner Rick Andre" devote themselves to killing Morty is funny just from the absurd lengths the aliens go to when Morty has no idea what the hell is going on. Then the season 5 finale showed that something very similar happened to Rick; a stranger came from a portal, destroyed all that he held dear, and Rick devoted his life to getting vengeance, so far to no success.
A lot becomes downright harsher when one sees the Season 5 finale "Rickmurai Jack":
Beth says she has a lot of abandonment issues about how Rick exited her life and came back as nothing happened. Rick in the meantime maintains that she uses her Freudian Excuse as a reason to not confront her own violent and assholish tendencies. As a result, Morty assumes that Rick is just a dimension-hopping asshole that takes his family for granted because Rick can always get a new family or a Morty even if he wishes. "Rickmurai Jack" confirms that our Rick lost his Beth when she was a little girl, meaning that he didn't abandon any Beth when she was young.
The alien marriage counsellor bemoans the tragedy of Beth and Jerry's marriage noting how they are so toxic to each other they should not be together at any cost. "Rickmurai Jack" reveals that this is because the Citadel of Ricks ensured that Beth and Jerry get together so that they could clone Mortys.
The season 3 premiere "The Rickshank Redemption" had Rick seemingly reveal his tragic backstory, only for him to say he was making it up for the purpose of staging a breakout. "Rickmurai Jack" has a shocker: the tragic flashback was real! Our Rick did lose his wife Diane and Beth when the latter was a child. That shock on his face as he was reliving the memory was not acting; he was actually responding to the trauma.
There's a bit in "Mort Dinner Rick Andre" where Nimbus calls out Rick for being a selfish apathetic asshole, telling him that his wife Diane wouldn't have liked the person that Rick had become. Rick becomes downright cold at Nimbus, telling him not to establish "canonical backstory" while the blow obviously hits. The season 5 finale proves that Mr. Nimbus was right; our Rick used to be more idealistic until an unknown Rick killed his wife and preteen Beth, prompting the former to go on a Roaring Rampage of Revenge and hunt down his family's murderer. By the time our Rick gave up, he devolved into the cynical alcoholic deadbeat father that our Beth knows.
In the first Interdimensional Cable episode, there is a subplot about an alternate Beth and Jerry who went their separate ways after Beth aborted Summer and both lived successful (albeit unfulfilling) lives. The fact that these alternate versions still end up together is heartwarming on the surface. When you watch the Season 5 finale, however, you learn that Ricks have been manipulating events across the multiverse to ensure that Beths and Jerries get together so that they continue to have a steady supply of Morties, it calls into question whether this moment was genuine or engineered.
In "The Whirly Dirly Conspiracy", Jerry calls out Rick for ruining his life and family. Rick rebukes this by saying that Jerry's home life would have ended up rather the same even without Rick's interference due to Jerry's victim complex. He also says Beth is "Rick's daughter" not "his or my daughter". It is revealed that the Citadel is responsible for setting up Jerrys and Beths together for the sake of creating Morties and the Jerry in question is just one of the countless Jerrys that was nudged into getting their Beth pregnant. Rick's phrasing regarding Beth also foreshadows how he really isn't her father. This is also why Rick saved Jerry instead of leaving him to die. He was projecting as he knows that he indirectly caused the pregnancy to happen in the first place.
In "The Rickshank Redemption", Morty takes Summer to his original Cronenberged dimension, and after his original family breaks their portal gun, a team of Ricks from the Citadel arrives and freezes all three of them (original Summer, Beth, and Jerry) in ice while arresting the main Morty and Summer. When Morty is forced back to his home universe in "Solaricks", he finds only Jerry still alive there, who reveals that Beth and Summer both died as a result of this, completely averting Harmless Freezing.
And then Hermit Jerry (the show's original Jerry mentioned above) is also killed in The Stinger by Rick Prime, meaning that, out of the five original main characters that we see for the first six episodes of the show, only the titular Rick and Morty are still alive.
This episode also reveals that Rick C-137 didn't crash land into Beth Prime's house because he was a Death Seeker beyond the Despair Event Horizon who was desperate for a family. All the Character Development of the last five seasons is... hard to take, because what really happened was he had found Rick Prime's home dimension and wanted to hunt him. The Character Development and attachment to family was all an accident. C-137 found it so easy to abandon Beth, Summer, and Jerry Prime, taking only Morty Prime with him, because they were all just part of the most hated dimension and not a family he had sought out.
Like the current Beth, the original Beth of the first six episodes had a whole bunch of emotional issues due to being abandoned by her dad when she was a kid. She believed that she got her father back when Main Rick showed up at her home not too long before the start of the series, as confirmed in the flashback in "Rickmurai Jack", as she didn't realize that he wasn't her original Rick, and was overjoyed to have him there. It turns out Rick only came there because it was Rick Prime's home dimension and he was hoping the latter would return someday so he could take revenge on him. He did end up sincerely bonding with Morty and kept him with him when he switched dimensions in "Rick Potion #9", but left the other family members there, meaning that Beth was abandoned again by a second, completely different version of her father, who, in the end, wasn't all that much more attached to her than her original dad was.
What's more, said original dad, Rick Prime, is one of the most sociopathic versions of Rick seen in the show so far, who not only doesn't give a shit about her or anyone else, but, when he's forcibly shunted back to their universe by the events of "Solaricks", murders Jerry, her husband, whom she had grown to deeply love in this universe up to her death.
A bit in-universe for Morty as well. Even after confirming in the previous episode that Rick isn't his original version, since Rick doesn't even have his own native grandkids in his dimension, Morty assumed that Rick chose the former's original home dimension to settle down in because the native Rick there was dead. Once Rick tells him the truth—that he came there because it was Rick Prime's dimension—Morty becomes worried that Rick may have only seen him as bait all this time rather than actually caring about him. Rick reassures him that it's not the case, and while that's pretty clearly true now, it does beg the question of how long it took before Rick stopped considering Morty to be someone he could use in any way to help him get revenge, and whether Rick bringing Morty and nobody else with him in "Rick Potion #9" had anything to do with said revenge.
This episode also confirms the long-standing fan theory that the second Main Jerry, the one the audience follows from the end of "Rick Potion #9", was accidentally swapped for a different Jerry at the Jerryboree in "Mortynight Run". We see here that the new version of the Smith family that he ended up with never went through the same Character Development as the versions that the audience follows. This means that all of the bonding moments Jerry had with Beth and other characters for the second half of Season 1 and beginning of Season 2—like in "Rixty Minutes", "Close Rick-Counters", "Ricksy Business", and "A Rickle in Time"—turned out to be completely for naught for him, since he ended up with a version of the family that remained unhappy and resentful of each other, and this Jerry (known as "Season 2 Jerry") likewise stagnated in character development once he left the main family (through no fault of his own, just a mix-up) and became part of this alternate one.* The current Main Jerry did at least experience most of the same events that happened in those episodes, so they weren't all for naught for him, but they still were for the second Jerry.
On that note, the same episode that confirms that the current Main Jerry is the show's third version of him also kills off both of the previous two versions. As mentioned above, Hermit Jerry (the first one) is killed by Rick Prime, and "Season 2 Jerry" (the second one) dies when he's bitten and assimilated by Mr. Frundles, who then takes over the whole planet. Essentially, if one were to rewatch any Season 1 episode, no matter which one it is, or the Season 2 premiere, the Jerry who appears in it is now dead.
In "Juricksic Mort", there's a Take That! towards Sean Penn's alleged history of abuse when Rick claims that someone who made a grave mistake like his would virtue signal as hard as he did. This becomes harder to laugh at after Justin Roiland's own domestic abuse charges came out a few months after the episode aired, which led to his firing.
