In the pilot, Rick mentions that he builds robots for fun. In "Something Ricked This Way Comes" we see one - a tabletop model whose only purpose in life is to pass the butter. It's sophisticated enough to be extremely disappointed at not being used for anything else.
Jerry is still wearing a suit after it's revealed that they were inside a simulation inside a bigger simulation. The suit disappears when it's revealed that they were actually still inside a third layer of simulation. Notably, this is possibly how Rick realized they were still in a simulation as he comments on it earlier and likely took notice of how it didn't vanish when they "escaped" the simulatuon.
Also, if you watch the episode a second time, the first one minute and twenty-four seconds are foreshadowing of the fact that Rick suspected that Simulated!Morty was a simulation all along, and the first line "this is just poor craftsmanship" referring to the possum he's dissecting is a complaint about the simulators - he's probably doing it to determine how many levels down he is.
Also, the alien simulation of Morty smiles knowingly as Rick brags that he's going to beat the aliens at their own game.
Also also, the aliens say that there's another human in the simulation, not a third human when they find Jerry. The language makes it ambiguous, but it sticks out on a re-watch.
Also yet again, Rick lampshades the Contrived Coincidence of Morty going into another room and immediately finding the exact ingredients for concentrated dark matter, because he correctly suspected they were still in a simulation. The recipe was fake, but the aliens cluelessly try it anyway and get vaporized.
It’s a little off for one of the ingredients for dark matter is water.
And if you happen to know about Physics, when cesium is mixed with water, it can go…KABLOOEY!!!
If you listen closely in the beginning, the aliens note that Jerry was in a different sector of the simulation and had to lower the processing power for him so Rick doesn't get wise. Later on we see that Jerry is in his own room on his own treadmill, which means he was in his own simulation independent to that of Rick's. However, this was before we find out that they were in fact in another layer of simulation, which explains why lowering the processing power in his separate room boosted that in Rick's room, since they're both technically in the same room the entire time. This is also why Jerry's simulation starts glitching out more and more, eventually freezing entirely, at the same time Rick successfully crashed his own.
In "Rick Potion #9", Rick's skewed view of love, being "just a chemical reaction that compels animals to breed" hints at what his love potion actually is. In the same scene, "I did it. Your parents are gonna do it." Everyone can see that foreshadows Jerry's and Beth's eventual divorce in Season 3, though they do later get back together. It also foreshadows the reveal in "Rickmurai Jack" that the Citadel of Ricks manipulated Jerrys and Beths across the multiverse into hooking up—sometimes even through the uses of some kind of love drug/pheromone—so they would eventually give birth to Morty. In other words, in many different universes, the "love" between Beth and Jerry was literally a forcibly-induced chemical reaction to compel them to breed.
"Rixty Minutes": Jerry and Beth's first trip with the goggles both being realities in dimension C-500 A.
Fart's song "Goodbye Moonmen" in "Mortynight Run" sounds like Word Salad Lyrics comprised of extraterestrial Technobabble, but it's actually about establishing peace throughout the universe by wiping out all carbon-based life. Moreso, while it's not clear until The Reveal, Fart's true intentions as a creature that intends to obliterate all life in the universe is made very clear if you pay attention to the seemingly-nonsensical lyrics and realize what lines like "we make sure they see the sun" and "we say goodbye, Moonmen" are truly implying.
The first memory being brought up is from Mr. Poopybutthole, about him and the family getting stuck in an elevator. Jerry and Beth getting into (yet another) argument, Morty almost pissing himself, and Summer having already pissed on her pants on purpose and getting dirty looks from the others for it all mean that this was definitely far from being a pleasant experience.
When everyone's going through their cellphones looking for pictures to show who is and isn't real, Mr. Poopybutthole says he doesn't have any of them either. We learn not long after that the parasites can only create POSITIVE memories, so him not having any would go against the nature of the parasites, and it's also notable that ONLY characters that are real check their cellphones for photos. This foreshadows that Mr. Poopybutthole is NOT one of the parasites.
In addition, despite Mr. Poopybutthole being inexplicably in the opening credits, it's notable that none of those memories would've been good. In fact, there's only one scene in the opening credits which is a "good memory": Mr. Beauregarde appears in the pillow fight, revealing the true original parasite.
Also, Rick's catchphrase montage is the first flashback of the episode to only contain real characters. It's also the episode's first set of negative memories, judging from the collective groan from the room immediately afterwards. This is an early suggestion that the parasites can't create negative memories.
Subverted by showing family pictures that only contain the real characters in the background of some shots, which are never used to solve the problem, and might have resulted in false negatives if they were.
When Rick starts ranting to Morty at the end, he states at one point that he's "not motivated to avenge my dead family!" and is only trying to get his hands on the McDonald's Szechuan sauce. Considering that Morty doesn't even know about the supposedly-fake memory of Rick's family dying, and nobody else made the suggestion of Rick trying to take revenge, either (since the G-Fed was focused on Rick inventing the portal gun), this feels like a Suspiciously Specific Denial. "Rickmurai Jack" later reveals that Rick's origin story was indeed mostly true (except for the part about him inventing the portal gun immediately after the bomb went off), and his motivation for most of his life since Diane and Beth were killed has, in fact, been to avenge his dead family, at which he, sadly, never succeeded.
Rick materializing butts around as a joke also counts as one, establishing that he can create fake things in his mind. The biggest aspect of his memory of his family's death that wasn't real was him figuring out how to invent the portal gun instantly after Diane and Beth were blown up, despite being shown just moments before to not have a portal in working order yet. This is something fake he created to break out of the simulation device and hijack his interrogator's body.
Also of note was that Rick correctly identifies which type of device is being used on him, including model number. It isn't a stretch to think that Rick knows the flaws and shortcomings of this particular device, allowing him to manipulate it easily.
Rick: "Six folds, huh? W-W-What, have you guys got me in a Series 9000? You cheap insect [bleep] didn't think I was worth your best equipment?"
In "Auto Erotic Assimilation", Unity tells Rick it cannot be with him because he is a toxic influence, telling him "I lose who I am and become a part of you". Fast forward to Season 3, Morty has become more hostile and rude to those around him, responding to bad situations with the same violent streak that Rick possesses.
"Morty's Mind Blowers": One of the memories includes Rick telling Summer he will do something to Morty's memory and she reacts nonchalantly. At the end of the episode, it turns out Summer is aware of the mind blowers, and is actually responsible for safeguarding Rick and Morty from possible scenarios (at least four) that might arise from them tampering with memories. Her response to the scenario being only little surprise implies that this is not the first time this has happened.
Season 4
In "Edge of Tomorty: Rick Die Rickpeat", Morty commits various crimes and almost alienates himself from everyone else to secure his future of dying together with Jessica, despite it growing impossible by the minute. Then The Stinger reveals that Jessica plans to become a hospice worker and comfort the lonely elderly people in their dying moments, thus revealing how exactly Morty could have 'set the future'.
In "Promortyus", Rick pointing out that there is an M&M Store comes off as a quick gag, but it reveals early on that the civilization had human influence.
Similarly, Spencer Grammer's voice can be heard as the announcer on the intercom praising Glorzo, indicating that Summer may have been involved in the mission before the facehuggers first latched onto Rick and Morty.
After Morty pulls down Goldenfold's pants and uses the remote, the shot lingers for a second after Morty vanishes, hinting at the fact that Morty is hopping between timelines instead of truly resetting, and that all of his actions still happened in the previous timeline.
A few different ones from Morty's interactions with Jessica:
In one timeline, when Morty just politely greets her, she ambivalently brushes him off and walks away, even though the Jessica we know is almost always quite polite to Morty.
In another, after he talks to her and walks away, she outright squees with delight, despite never being that excited about talking to him before.
When he later apologizes to her for this behavior, she says she doesn't know what he's talking about. At first it might seem like just casually brushing aside the apology, but in hindsight, she clearly means it literally; the Jessica he's talking to now is not the same one as the above example.
Shortly before it's revealed that Rick and Morty are in a parallel reality at the end instead of their current home reality, the judge whom Morty apparently drove to suicide in "Edge of Tomorty: Rick Die Rickpeat" shows up alive and well in the mob out for his blood.
Before Rick reveals to Morty that he's not "his" Rick, and Morty is currently in another dimension, the entire scene with this alternate Rick has him talking a little slower and with slightly different intonation than the Rick we know.
There's also a blink-and-you'll-miss-it foreshadow of how the device works right when Rick first "uses" it. When Rick hits the button he is frowning and glaring at Morty, but when he "resets to that exact same moment" he now has a different expression and is looking away instead, because this is another Rick who is in on the plan and waiting to take our Rick's place rather than a Morty who was naturally in that same place at that exact same time due to a branching probability in time.
The episode "Childrick of Mort" (a shoutout to Children of Men) has the family dealing with the fact that Rick may have gotten a planet pregnant. When the children come flying out of a geyser in large numbers, they're all crying "I AM!", a hint that they were fathered by a god. ("I Am" is one of those super pretentious names for god in the Bible. "Before the Father was, I am" - Jesus)
Season 5
The "Central Finite Curve" is a concept mentioned and introduced in two episodes—"Close Rick-counters of the Rick Kind", where the Council mentions that of "all the Ricks" in the Curve, our Rick is the rogue, and "The Ricklantis Mixup", where it's mentioned that Simple Rick exists sixty iterations from the Curve. Besides being episodes dealing with the nature of the Citadel and alternate Ricks, these are also the two episodes where Evil Morty makes an appearance. In "Rickmurai Jack", it's finally revealed what the Central Finite Curve is: a section of the multiverse consisting only of universes where Rick is the smartest man of all, and Evil Morty's motivation is to break the Curve and escape into the true multiverse, free of Rick's influence.
Season 7
In "Fear No Mort", There's a few hints about the true greatest fear the hole wants addressed.
Rick is never actually seen jumping into the Hole from the outside, he just falls into Morty's view while he's already in the Hole after Morty cries out for him.
Morty asks what Diane coming back has to do with him. Rick responds after a pause that perhaps Morty's greatest fear is that Rick will find happiness again and no longer need him, claiming that Morty's getting scared just talking about it. Morty adamantly denies it.
Rick states that they cannot know for sure without more data, starting a long montage of Rick and Diane reuniting and falling in love while Morty feels increasingly sidelined. He also notes that he's only doing it for Morty, so the sooner he finishes his romance arc Morty can focus on his fear of being a "useless, lonely little turd".
As Rick shows signs of deterioration, Morty theorizes his greatest fear is watching Rick die. Rick, a manifestation of the hole says he likes this theory, telling him to stop watching. This leads Morty to another encounter with the Rod SterlingExpy who gives further hints that fear of losing happiness and the inevitability of losing a loved one is the central theme of the episode. He also claims that Morty does not matter, dismissing him as a secondary character.
Rick's arc parallels Morty's, confessing that his greatest fear is letting a loved one go. In the end when confronted by Diane about the possibility of losing her again and whether or not Morty is even real, Rick chooses to sacrifice himself for Morty.
The final sequence entails Rick and Morty trying to figure out whether or not they are in the hole include Rick asking Morty to confess his fears, Morty confessing that he's afraid he's responsible for Rick's sadness, Morty seeing a montage of him growing up (and apart from Rick) until he realizes he's afraid of becoming normal like his father (struggling with a mundane life in the corporate world and with age).
In General
Comics!Rick and Morty world is rarely mentioned in the series, despite there being a Morty smarter than his Rick as well as an incident where Jerry took over the Citadel of Ricks, which will doubtlessly affect the dynamic between Rick, Morty and Jerry. 'Rickmurai Jack' explains why: those universes were outside the Central Finite Curve (where Rick is always the smartest man in his universe) so Rick and Morty from the show never knew these scenarios even happened.
In "Close Rick-counters of the Rick Kind", Morty is never referred to as C-137, even though "our" Rick is. Later in "The Rickshank Redemption" when he gives that as his dimension, the guard Ricks look surprised to hear it. This is because the Morty of 'C-137 Rick's' home dimension never existed, due to his mother dying as a child.
In the same episode, Rick offhandedly mentions to Morty that he's extremely important to the other Ricks because of his brainwaves, which enables Ricks to evade their enemies and launch a surprise attack on them if possible. Four seasons later, this is revealed to be the actual reason behind Morty's entire existence across infinity: the Citadel manipulated Beth and Jerry so that they have infinite Mortys to use as sidekicks for their brainwaves.
During Beth and Jerry's marriage 'counselling' back in "Big Trouble in Little Sanchez", the counsellor expresses his disbelief and indignation, outright stating they are the worst couple he has ever seen, zero compatibility, and shouldn't even exist. In "Rickmurai Jack", we learn that the counsellor was accidentally right, Beth and Jerry could never have gotten together in ordinary circumstances. The Citadel of Ricks was responsible for Beth and Jerry to be together so that they could birth Morty as 'the perfect sidekick'.
