Practically any time you see Cheryl's pet ocelot, Babou, sitting alone without a single thing to play with except his food and water dish.
Archer's childhood was disappointment after disappointment, and was scarring enough to make him the person he is today. Most of the flashbacks to his past we see are quite sad. For example, when he talks about how his boarding school/lacrosse buddies were like the family he never had, and then it cuts to him as a child, sitting alone on the bench with his net, and when he did get attention from other boys, it was vicious emotional and physical bullying, so bad that at one point it even put him in the hospital. When Malory finally showed up in his life after being completely absent for his first 5 years, he claimed he didn't have a mother, and if he did, he would hate her. Oh, and not to mention, he went through statutory rape ala his nanny when he was 12. Jesus.
Though it's often not played completely seriously, Cheryl's childhood was horrible. Surrounded by racists, domestic abusers, child molesters, rooms full of weapons and general neurotics and bastard people, and combine this with her mental illnesses and sexual abuse by her grandfather, when you take it all into account, it makes sense as to why Cheryl can be a little bit off her rocker.
As hilarious as it is, Brett constantly getting shot and beaten with everyone around him (including the perpetrators) responding with either amusement or apathy is kinda sad.
Brett: I don't think I have any blood left...
The death of George Coe, the first voice of Woodhouse. The tribute they gave him on their Facebook page is actually really touching and ends with the scene where Archer actually admits to Woodhouse that he respects him (from Stage Two) and the words "Thank You George Coe. " Thank you.
In "Training Day," Archer saves a guy from an assassin. The guy, wearing a red-bloused military uniform and sporting white facial hair, thanks him profusely, to which Archer replies, "I love you Santa Claus! [holds his hand to his face to cover sudden tears] I do..." It's played for laughs, but when you think about the fact that Santa loves all children, and that Archer grew up never knowing his father and with a mother who shows more affection for her dog...
"Tragical History" gives us a glimpse into Cyril's childhood, when he embarrassed himself and disappointed his father at a spelling bee. Doesn't help that the flashback is followed up by how he's being abused by his friends in the present.
Really, the entire episode can be considered a Tearjerker, considering Cyril being put down continually left and right. Sure, he put ISIS at risk, but can you blame his motive?
"Placebo Effect" where Archer meets an elderly woman named Ruth, at the pharmacy when they're both collecting chemotherapy drugs, and befriends her. Since they turn out to be fake, the cancer ends up killing her. This is implied to be Archer's main motivation for going on his revenge fueled rampage.
"Delaney. Did you see Regis this morning?"
Pam's whole ordeal in "El Secuestro". First, Cheryl made her kidnappers think that Pam was her so she wouldn't be kidnapped. Then Pam is subjected to a brutal beatdown, and when ISIS negotiate for her release, Malory only offers up $5,000. When Pam and her kidnappers arrive at ISIS headquarters, none of them drop their guns when ordered to do so, even though the leader has a gun pointed at Pam's head. And after it's all over, Pam lets out an anguished cry if any of them even care about her before beating Malory for what she feels is worth $5,000.
"Double Trouble" and Season 2's overall sheer Downer Ending. Thanks to his meaningful relationship with Katya, Archer has become a much better person, and the two are about to finally get married atop Archer's roof when Barry, now a cyborg, bursts in and grabs Archer in a choke-hold and dangles him off the roof. Malory unsuccessfully tries to stop him, and as a last-ditch effort, Katya grabs Barry and dives off the roof into the street below, saving Archer's life but sacrificing her own. The episode ends with Archer sobbing and screaming out her name over the balcony as Barry boasts from the streets. It's one of the most uncharacteristically saddening and serious moments for the show, and is all the more effective for it.
In "Crossing Over", Archer finally starts to bond with Nikolai Jakov, his possible father. Barry, now the head of the KGB in Jakov's place, travels to New York, manipulates Cheryl into taking him to the ISIS safehouse, and tells Jakov that he will kill him. Jakov seems content to die, as long as Archer will be able to go through with the test to see if Jakov is his real father. This isn't enough for Barry, and he sets up a fork enclosed in ice in the microwave, and creates a gas leak, so that the entire building will explode and Jakov's corpse will be too disfigured to test on. Jakov tells his remaining secrets to the debriefing camera in case it survives the explosion, but is notably upset that Archer will never find out if Jakov is really his father of not.
"Skin Game" isn't much better: Although Archer and Katya are reunited through Krieger's secret project, she eventually runs away with Barry due to the physical differences between her and Archer.
In "Vicious Coupling."
Archer: Geez, Lana. That is the third saddest thing I heard today. Pam told me about a little girl who died trying to save a puppy.
Lana: JESUS. What was the SECOND saddest?
Archer: (voice cracking) The puppy drowned too...
Lana: (covers her mouth, shocked)
Hell, the entire reveal that Katya was using Archer to get Barry off the moon.
Ray reveals in "Once Bitten" that his father forced him to kill a bear with a bow and then eat said bear's heart. His dad kept hitting him until he finally did the deed. He cried the whole time.
Archer's dejected sigh after he forgets his father's face.
In "Sea Tunt, Part 2":
The Reveal that Captain Murphy is all alone and has gone mad. The moment when Lana realises is one of the downer parts of the episode, particularly since Murphy dies (in a slightly comedic way, mind) before he can escape.
Lana: How long have you been down here?
Archer's Heroic Sacrifice to save a pregnant Lana and subsequent (temporary) death via drowning is extremely sad, especially Archer's last words as the water fills his lungs:
In "White Elephant", Lana tells Archer she'd rather lose her unborn child than marry him. Even she seems to realize she went too far once he sheds a few Manly Tears.
Ramon's death in "A Kiss While Dying", and Archer kissing him to fulfill his dying wish. Even though Ramon, Charles and Rudy faked the whole thing, we didn't know that at the time, and it was still a touching moment.
In "House Call", Lana bursting into tears upon learning that if she were to be sent to jail, her baby would be taken from her the moment it was born.
Ray's grief over losing the ability to walk again.
Ron leaving Malory after putting with all the chaos.
After mistakenly thinking the cocaine (from Pam) was yogurt, Archer gives a horrified gasp over thinking that kids like it.
In "Southbound and Down", Malory says to Cyril and Lana that Archer is somehow a worse drug smuggler than he was a field agent, only to discover that Cyril had the radio switched on and he heard the whole thing. Archer's stunned attempt to shrug off how little his mother thinks of him is actually pretty tragic. Made worse by the fact that this is probably a glimpse at feelings he's dealing with a lot but never really mentions.
In "Smuggler's Blues", Malory breaking down and pleading to Lana to get Sterling back when she believes he's in danger.
"Palace Intrigue: Part 2":
Krieger, abducted by his clones, overhears the others commenting that they don't care that he's missing. Does Krieger get mad and call them assholes? Nope. He breaks down and weeps like a child. It really hurts him that the people he views as his friends care so little about him.
Archer's cracking voice when they think Pam is dead.
Everyone's horrified, tearful or enraged reaction when they think Pam is dead.
Lana is giving Archer a heartfelt speech but he's incapable of hearing it. It's a bit sad that she seems to pour her heart into the speech and the guy she's telling it to won't know what she said.
In "The Holdout", the season opener, Archer finds an elderly Japanese WW2 soldier who's under the impression that the war isn't over. As funny as the running gag of Archer explaining to him what he's missed (including how The Six Million Dollar Man had this same plot) it turns to sorrow when the soldier learns about the two atomic bombs dropped on Japan and thinks his wife and child were among the casualties. Happily, the episode ends on a heartwarming note when Archer uses his phone to track down and call the soldier's wife and reunite them.
In "Edie's Wedding", even though nobody would be sad to see him go, it is kind of sad to see Barry go completely insane after Katya leaving him for Boris.
In that same episode, seeing Pam constantly getting torn down and insulted by her own sister. And it's implied she and Edie have had this kind of relationship since they were kids.
Crossing over into Fridge Horror, how Edie, as a grown adult woman, still thinks all the shit she did was hilarious, and continues to do it.
In "Reignition Sequence" Archer decides to make dinner for Lana when he comes home and Woodhouse is still missing his line becomes Harsher in Hindsight given George Coe's death shortly after this.note Tom Kane replaced him in Archer Vice
Archer: Unless you came home you little scamp. Woodhouse?! Woodhouse! Seriously I hope he didn't die.
"Drastic Voyage Part 1 and 2" has Ray in tears after being handicapped again, stuck with a bionic hand on top of his now inoperable legs, and he's been Mistaken for Racist because everyone thought he was complaining about the hand being African-American.
In "Deadly Prep", there's the scene where Archer delivers a hauntingly detailed account of an incident in which he was beaten by two larger boys in the school locker room and held upside-down in an unflushed toilet, begging them to stop before blacking out from inhaling water, urine and blood, ultimately resulting in pneumonia and an extended hospital stay. The scene is not played for laughs in any way and does not lead up to any jokes of even the black humour variety, just cutting back to a genuinely shaken Archer and a remorseless but taken aback Ivy.
The apparent death of ARCHER HIMSELF at the end of the season finale.
The opening scene of "No Good Deed" is a grey, rain-swept funeral, but it's not Archer's, it's Woodhouse's, who'd been missing ever since Season 6.
Priest: Oh death, where is thy sting? Oh grave, where is thy victory? For man who is born of woman have but a short time to live, and is full of misery. He cometh up, and is cut down like a flower. He fleeth as it were, a shadow. In the midst of life, we are in death. In the midst of death, we are in life...
It turns out Archer's not dead, but has been in a coma ever since Veronica Deane tried to kill him, which by "No Good Deed" was three months ago. It's implied Malory has been by Archer's side for most of that time, refusing to leave because she wants to be there when he wakes up despite the slim chance of it ever happening. There's no absolutely no humor between Malory and Lana as they discuss Woodhouse's passing and Archer's comatose state, with Lana showing concern for Malory's well-being and Malory telling her she's fine. Lana then says she'll bring A.J. with her to say Archer the following day... or later in the week, implying Lana's having difficulty with showing A.J. what's happened to her father.
The way Malory says "I want to be here if... when he wakes up." Followed by Malory saying she, and Archer, will be there whenever Lana decides to bring A.J. with her in a resigned, defeated tone.
Lana hopes that Archer being comatose means he wouldn't know about Woodhouse's death because it'd destroy him, but Malory wonders what Archer's capable of hearing and knowing despite not being conscious. True enough, he seems to know on at least some level, because in "Dreamland" we see Archer discovering someone has murdered his "partner" Woodhouse and being completely devastated.
Archer's rant at the end of "Gramercy, Halberd!"
''I always do shit like this! All I wanted to do was find out who killed my partner, Woodhouse, and the next thing I know, I've disappeared up my own asshole, and I'm manumitting sex slaves, and grossly abusing corpses, and trying to sort some finger for some weird psycho-sexual kidnapping, and then, to top off all the bullshit, getting chased by goddamn robots! I mean, fucking halberds, Jesus Christ!
Then, Trexler tells Archer that Mother killed Woodhouse.
The Chinese women leaving Poovey. Even sadder is that it's the closing scene of the season.
Hell, the whole season finale is largely a tear jerker. Archer gets nothing for his troubles (except for finding out Barry murdered Woodhouse only because the later cut him off in traffic), Pam accidentally shoots Lana to death, Kreiger's beloved cyborg dogs die by Zirk's hands due to turning on their master, Zirk saves Cheryl's life but his affections are cruelly rebuffed by her, and the briefcase with the money turns out to be filled with German nudism magazines.
The season ends with a farewell to George Coe.
Amid the escalating insanity, we get a moment where a baby monkey finds its mother has been shot dead.
Archer starting to see his dream crewmates as the canonical Archer series characters is pretty moving. It's been three years since we've seen them.
Archer hallucinating Woodhouse. As he approach the end of his coma, he hallucinates the one person who died at the start of it, and because it's at the end of the episode before the finale of the season, one can think that Archer is in a life-and-death crossroad, with the dead people visiting him before his awakening.
Archer realizing he was asleep for three years, he freaks out. Mallory and the nurse even have to hold him.
Archer awakens from his three years coma only to see his mother literally LIVED in his room. Sterling looks very concerned about his mother, and even if it looks like Cringe Comedy at best, her creepy last lines looked like she was getting a little insane from all the worrying about her son's condition. It's painfully tragic.
We don't know the situation for now but it looks like Mallory and Lana's friendly terms at the start of season 8 deteriorated of some sort, seeing Mallory's reaction when Archer mentions her.