The look on Daniel's face when he realizes that Sha're has been taken as a host.
Daniel saying goodbye to the people of Abydos, and telling them to bury the gate forever. He's crying the entire time and you realize that these people and this community have become his family, and he would rather be alone again than let something happen to them.
"The Enemy Within":
Subverted initially - Charles Kawalsky, who seems like a major character, is in great pain in a hospital bed. The music takes a distinctly mournful tone. Jack, with the saddest, most genuine look of sorrow on his face asks him, "If you don't make it... can I have your stereo?" Kawalsky, and the viewer, choke out laughter. Then, he actually dies in a heartwrenching, senseless way, one of the three characters who survived the film.
Jack repeatedly calling Kawalsky by his first name throughout the episode, leading the audience to realize just who Jack named his dead son after.
"Fire and Water":
The ending, where Nem uses his memory machine on Daniel to find out the fate of Omoroca (his mate) from ancient Babylonian texts. Finding out that a loved one has died is never easy, but finding out after waiting four thousand years hoping for their return:
Daniel: And in that place there was Omoroca, a woman who came forth from the heavenly egg, who walked among men by day. But at night she would retreat to the sea to sleep — one of the beings called Ohnes. The godBelus came down onto Babylon unto the place of Omoroca... and cut the woman asunder!"
Daniel Jackson's funeral.
Half of the episode is devoted to showing how much the lives of Jack and his ex-wife were impacted by their son's death.
At one point the crystal-energy doppelganger visits Charlie's room and relives Jack's memory of his son's death, and comes out the other end a sobbing, shaking wreck. It becomes more potent when, later on, the crystal Jack says that physical death doesn't have the same meaning to its kind, so it's experiencing a grief that it never even comprehended before.
When the doppelganger reveals that its entire mission was to help Jack, and explains that it deemed his emotional pain of losing Charlie to be greater than any physical injury he had. It explains that its goal was to go and get Charlie and bring him back to Jack to make him better, which is heartbreakingly childlike logic. That revelation in an of itself is awful, but then the doppelganger turns into Charlie to at least try and fulfill its mission and give Jack one last moment with him. The look on his face says it all.
"Torment of Tantalus": Earnest, having been alone on a world for 50 years with no human contact, hugs Daniel and says, tearfully, "About time."
"Cor-Ai": Teal'c accepts that he should be executed for his former life as the First Prime of Apophis. During his conversation with Jack about his guilt, he spends the entire time looking down, lip quivering, near tears. This is a man who rarely, if ever, shows any form of emotion.
Sam is ordered to leave Cassandra in the reactor silo, since the Goa'uld bomb in her chest is about to go off.
Cassandra: You promised you wouldn't leave me. You promised. Sam: I know... but I have to. Do you understand? (choking back tears) Just remember, you're very brave...
The look on both their faces as Sam closes the blast door, Sam crying her heart out on her way back up the elevator, and then turning the elevator around and going back to wait out the timer with Cassandra is one uninterrupted seven-minute stretch of tearjerking.
Earlier, Cassandra sees the team tagging the dead and takes one, and is later shown putting the tag on herself, essentially marking herself as dead.
The end of "Tin Man", when androids who, essentially, have the minds and identities of SG-1, agree to live in exile.
The reason Harlan created the duplicates in the first place. He's been all alone on his home planet, for years.
"There But for the Grace of God", especially the part when General!O'Neill is killed. He just kinda stands there in a daze as it happens.
Skaara's brief return to consciousness after a year as host to a Goa'uld in the first season finale is pretty painful. "O'Neill, are you still my friend?" Sob.
Not to mention the pained scream when Jack is forced to shoot him.
Daniel being left behind in the season 2 premiere (although Jack's face just made it worse; Daniel seemed pretty calm about the whole thing), etc.
The scene with Daniel's parents in "The Gamekeeper", absolutely every moment.
All of Daniels interactions with Sha're in "Secrets". He spends a good amount of time being upset and confused by the whole situation and its hard to see him and Sha're dancing around each other, unsure of what to do. Then of course he realizes he may only have a few days with her, and every moment between them becomes this as they try and find a way to protect her and get her back to Earth.
And then they fail, and Daniel has to watch as Sha're is overtaken by Amaunet again.
It's also heavily implied by the end of the episode that Sha're is still in there, fighting against Amaunet, as she makes eye contact with Daniel hiding behind a pillar, but doesn't give his position away, protecting him from Apophis. And from what we've seen of hosts who manage to regain their selves, that's a fate worse than death.
In "A Matter of Time", when Jack realizes that the thing Henry Boyd's team are so afraid of on P3W-451 is a Black Hole. Made even worse because Jack was the one who recommended him to lead SG-10 and it was his first mission through the Gate. The look of guilt on Jack's face says it all.
Then his furious What the Hell, Hero? to Carter, when she becomes almost giddy at the prospect of being the first to observe the effects of spaghettification, pointing out all they will see is good men dying horribly. Cut to the MALP, which is now showing Henry Boyd frozen in time, screaming in terror.
Jack refusing to forgive Cromwell for leaving him for dead during the Gulf War, which meant he spent some time in an Iraqi prison. Then shortly afterwards, Cromwell's safety-line snaps and he gets pulled through the gate.
Just the mere idea of what things would be like for poor SG-10, desperately trying to make it through the gate, only for it to close almost immediately, dashing their last hope of ever returning home alive.
"Serpent's Song" has a gutwrenchingly beautiful moment where Daniel is comforting the poor, thousands-of-years-old scribe who was Apophis' host by telling him that he will give him the final rites and that he will see his wife again after he dies.
"Show and Tell", when Re'tu!Charlie asks if Jack can be his dad...sniff.
Him asking to be called Charlie in the first place.
In fact that entire initial meeting from the moment the kid first mentions him having a son looks almost physically painful for Jack.
Then poor Re'tu!Charlie has a front row seat to his "mother's" murder.
Hammond being genuinely upset, to the point of his voice getting choked up, when Ma'chello suggest that they effectively sacrifice Daniel for his use. Seeing as Daniel is trapped in Ma'chello's old dying body, this is would be a death sentence for Daniel. It's always clear how much he cares about Jack, but this is the first time we really get to see his affection spreading to the rest of the team.
More of Daniel: when he is temporarily schizophrenic in the episode "Legacy", the team comes and visits him while he's institutionalized. He looks up at them and tearfully whispers, "They took my glasses..."
Quite a lot of 'Forever in a Day".
Sha're's death at the hands of Teal'c is uber heart-wrenching to watch.
Daniel recounting how Sha're was fascinated by his pen when he first arrived on Abydos has Carter in tears. Its clear just how much he loved her.
Him explaining his reasons for leaving to Jack as he packs his office. Specifically when he says that every time he stepped through the gate, he always wondered if this world would be the one he found Sha're on, and now that part of him won't exist anymore, that hope. It will just be another place, and he can't do it anymore. And then he starts to cry. He manages to get it under control, but my god, it's one of the most painful moments to watch.
Even though his team members are only creations, figments of his imagination, they still behave according to how Daniel would reasonably expect them to. So seeing both how they react, and how Daniel knows they would treat him in this very real scenario is both heartwarming and terribly sad.
Despite the fact it's all in his head this is still Daniel's process of moving through his grief.
Seeing what he would have done without Sha're's intervention — quitting the SGC, refusing to forgive Teal'c, cutting of communication with his team — is awful when you realize that that would have been his fate without her sending her last message.
His anger at Teal'c, while understandable, is horrible to see. It's clear just how betrayed he feels.
When Jack is under the influence of Apophis' hallucinogen and he sees a memory of when Charlie surprised him with a squirt gun. 'Charlie' wastes no time telling Jack that his original response was a lot harsher than what he says in the memory and that Charlie would accidentally shoot himself in the near future. Richard Dean Anderson really sells just how painful this is for Jack, who just asks Charlie if they can play catch like he'd originally intended that day. Of all the hallucinations Apophis puts SG-1 through, this is probably the cruelest, especially when Charlie smugly holds that happy what-could-have-been for ransom.
"Learning Curve", seeing the result of Merrin's 'averium' on the population of Orban is a good version of this. She went through with her sacrifice, and as a result, when SG-1 returns, they find corridors full of children laughing and playing, finally having learned fun. Even the adults are now seen enjoying their lives, the previously stoic Kalan having drawn a 'representation of himself' for the team. And all because of one little girl.
But of course because of this, the previously articulate and intelligent Merrin has been reduced to a mute, infant-like state, scribbling on the walls.
"Maternal Instinct", Daniel having to make the decision to leave Sha're's son in the hands of Oma. It meant having to come to terms with the fact that he wasn't able to completely fulfill Sha're's dying wish for him to protect 'the boy'. It's also him having to say goodbye to that last piece of his wife, and a child who was, in a way, his son too.
Even though they got out, Daniel blowing the sub that Jack and Teal'c were on in "Small Victories". Then, inversely, Jack blowing up a ship that he thought Daniel was on in "Scorched Earth".
The end of "Window of Opportunity". When they are trying to get Malakai to shut off the machine, he says that he wants it so he can see his wife again, believing that Jack could never know that kind of pain. Cue Jack's patience finally evaporating;
O'Neill: I lost my son!I know! And as much as I... I could never live through that again. Could you?
Then there's the story of the device he's using. The Ancients who lived there built it to prevent some catastrophe from wiping them out, but it only ever looped time a few hours. After countless attempts to make the device work, they gave up and let the end come.
That this caps off arguably the most comedic entry in the series' entire history makes it all the more heartwrenching. There's a reason why Window of Opportunity tops almost every fan-favorite episode list.
The end of "Divide and Conquer", Poor Martuf...
Loren's story from "The Light" is pretty awful. Poor kid.
What about Jack walking in on Daniel about to jump off his balcony, complete with him tearfully saying that it 'doesn't mean anything'. Its revealed in the next scene of course that this is due to some weekly alien shenanigans, but because of all the awful stuff thats happened to him, it is genuinely believable for a moment that Daniel might actually jump.
When he 'wakes up' from his little trance and realises where he is, he sounds so scared.
Daniel being unable to talk about what happened to Sha're in "Absolute Power".
His held gaze with Shifu at the end. The kid was sort of his son, and protecting him was Sha're's dying wish, so its understandably hard on Daniel.
The ending to "Double Jeopardy", all of the robotic duplicates have died. Each one committing a Heroic Sacrifice in order to help the original team.
Robot!O'Neill: Are we still so far from real to you?
O'Neill: (sadly) No, I guess not.
Robot!O'Neill: Then I believe we're done... (dies)
While it's not mentioned, Harlan was likely left heartbroken upon learning of their deaths.
General Hammond's conversation with Jack about Teal'c's fate in "Threshold". Due to his involvement with the Stargate program, he would have to be put in a maximum security prison in solitary confinement for the remainder of his life, which, given his reliance on the infant Goa'ould, will likely only be another 4 or 5 years. After that, he will die in agonising pain. Hammond keeps up his stoic exterior while explaining this, but he admits that he can't do that to Teal'c.
Hammond: I won't do that to him Jack
Hammond's reluctance to enter the room while Teal'c is being deprogrammed. It clearly really hurts him to see a man that he trusts so much and has so much faith in reduced to such a state. And once its over, he immediately runs into the room, on the edge of crying.
Daniel yelling at Jack for killing Reese. Its sad as Daniel really did seem to care for Reese and is mourning her, and it's also sad seeing Daniel and Jack so angry at each other. Specifically Daniel calling Jack a stupid son of a bitch. He has only shown that much contempt for a Goa'ould.
This episode was a real soul-crusher for the fans.
From the same episode, Daniel repeatedly telling Oma he doesn't believe he's done enough good. His open honestly about how deep he is into the Despair Event Horizon eventually causes the eternally cryptic Oma to drop the koans and just tell him one truth: that the only thing he ever could control was whether he was good or evil.
Sam wondering around Daniels empty office in Revelations.
Hammond trying to console Sam about Daniels uncertain fate by telling her about his friend who got shot down in Vietnam, managed to pull his 'chute, but was never found.
In sort of a happy way, that last breeze going past the gang as they all leave for the night. Daniel's subtle way of telling them he may be dead, but he's not gone.
Calling the first hyper space capable earth fighter jet 'Abydos 1'.
Jack and Daniel's conversation in "Abyss" while Jack was being tortured by Ba'al and Daniel was dead. It alternates between hilarious and heartbreaking.
Special mention goes to Jack yelling at Daniel that if their positions were reversed he would break Daniel out in a heartbeat. And then he would make Ba'al suffer. When Daniel says he wouldn't because he's a better man than that, Jack immediately screams at him 'That's where you're wrong!", Once again hammering home the point that when it comes to his little adopted family, there isn't much he wouldn't do. Even if they are already gone.
At one point while being tortured, Jack's reduced to simply whispering Daniels name, begging him to end it.
After the scene mentioned above, when Jack is back in the prison, he very quietly asks for Daniel, and then says so sadly 'you were gone'. It almost feels like he's talking about life in general, rather than this specific situation, with his little brother figure Daniel having gone, and Jack being a bit lost without him.
The Tok'ra aren't always entirely sympathetic, but the events of "Cure" not only bring home their plight (they are in a very real way a dying race), but with their reaction to Egeria and what has happened to her, plus the fact that she's dying, all over a stupid, impossible to foresee mistake, also remind us that they aren't just arrogant, unfeeling dicks. Malak, for one, looks near to tears when Egeria tells him that she's dying and gives her So Proud of You line. Because after all, Egeria is his mother, the mother of all the Tok'ra and they found her again just in time for her to die, despite all they tried to save her.
How about the look on Fifth Replicator's face end of "Unnatural Selection" when he realizes Carter and the others are leaving without him.
Teal'c comforting Sam in the locker room when Jack is MIA.
Daniel promising Teal'c that when he wakes up everything will be fine.
All of Jonas dealing with his old professor friend, Dr. Kieran in "Shadow Play". The poor man is firmly in the grip of his hallucinations (a result of long-term exposure to radiation from naquadria), and Jonas just doesn't have the heart to tell him the truth.
The beginning of season 7, when Daniel returns from the dead and doesn't remember his team. There's this moment where he just sort of shrugs, says they don't look familiar, and walks past them. The look on Jack's face is plainly heartbreaking.
Later in the same episode, Daniels jubilation at being able to remember Sha're's name is abruptly bought to an end when he relearns that she is dead. He looks down at the photo of her he's carrying and says, voice breaking slightly, 'I loved her very much'. He then places the photo face down next to him and changes the subject.
In "Fragile Balance", when you realize that Jack's clone is roughly the same age that Charlie would have been...
Poor little Keenan in 'Lifeboats' telling Janet about his Mum.
The seventh-season episode "Heroes".
The death of Doctor Janet Fraiser, that is all.
Sam's general emotional state in part 2 is pretty hard to watch. Teal'c coming to her nearly crying, having written a eulogy also qualifies, and Daniels protectiveness over the tape that shows the event are all big hits emotionally.
Also Daniel recounting the story of how he died, and how dedicated Janet was.
General Hammond's protectiveness during this whole time period, but especially him telling Sam that although you're supposed to care for all your officers equally, you can't help but care for some of them more. Its clear that he means SG-1 and Janet are officers he's come to care for more like family, and that the loss of Janet is hitting him particularly hard.
The second half of the "Heroes" two-parter. The whole episode revolves around the death of one character. The audience is led to believe it's one character. At the end, it is shown, in startlingly undramatic and completely heart-shattering frankness, that it was someone else.
It really is the manner in which we find out, in the very brutal and realistic lens of a battlefield camera, without the gloss of tv and hollywood.
The in-show tribute video at the end actually did bring tears to General Hammond's actor, a former Vietnam-era army sergeant. And for the regular viewers... fan-favorite regular Dr. Fraiser is killed instantly while treating a wounded airman during an offworld firefight. Samantha Carter delivers her euology.
We often talk about those that give their lives in the service of their country. And while Janet Frasier did just that, that's not what her life was about. The following are the names of the men and women who did not die in service, but who are in fact alive today because of Janet. Major Samantha Carter, Dr. Daniel Jackson, Colonel Jack O'Neill, Teal'c, Sergeant Connie Smith,Major Ian Hules, Senior Airman Simon Wells. . .
And the end of the episode when Simon Wells, the airman that Dr Frazier died saving, is revealed to have named his newborn daughter Janet after her.
"Lost City" closing with Jack frozen in the Ancient outpost.
"Avatar" can be brutal to watch, as Teal'c suffers slow mental exhaustion after becoming trapped in a computer simulation that will not let him win. He "dies" over and over again, no matter what he tries, and finally suffers a Heroic BSoD when he realizes the game won't even let him quit. It gets worse when it's revealed why he can't beat the simulation: the program's not malfunctioning. It's learning from Teal'c's personality and experiences, and tailoring the simulation to fit them. The reason Teal'c can't beat the Goa'uld in the game is because subconsciously he still believes that he'll never be able to beat the Goa'uld in real life.
That, and watching the virtual SGC personnel die over and over again. It's true they aren't the real people, but still...
When Sam's dad Jacob died for real.
"Avalon", watching as a poor terrified Vala is burned alive. All while Daniel is pleading with the people that they only wanted to meet them in peace.
Harrid and Sallis dying in fire near the end of "Origin", after having just switched back with Daniel and Vala.
The destruction of the Prometheus in "Ethon", complete with Pendergast's Heroic Sacrifice.
The worst part is that after years of service, and having saved at least two galaxies from annihilation. Prometheus is lost and the civilization it was destroyed trying to save wiped themselves out hours later. Talk about a Senseless Sacrifice...
Gerak, also in The Fourth Horseman. Gerak is made a Prior, Teal'c talks some sense into him and has him agree to help on Earth with the plague, but the Ori put a failsafe in their Priors that causes them to self destruct if they betray the Ori. "If I help you, I will die. But I WILL DIE FREE!"
The episode "Flesh And Blood" opens with apparently killing off Colonel Chekov. While it's never outright conformed if he was or wasn't one of the six people aside from Daniel who managed to evacuate the Korolev before it was destroyed. He's never seen or mentioned again. While he was often far from likeable, that's still a bit tragic.
The Ori invasion begins with Chulak being decimated. Teal'c and Bra'tac are horrified by the sight.
From "Counterstrike", when the team think Adria is dead Daniel assumes Vala is heartbroken over it. Turns out it's worse, while she is saddened over the loss. Vala explains to him that she had been holding herself at least partially responsible for Adria's actions. Daniel tries to comfort her, but doesn't have much success.
The loss of Dakara.
During the ending, Carter mentions that Langara and Hebridan are among the planets that have fallen to the Ori and that they haven't been able to get in contact with their allies there. Which means the fates of people like Jonas Quinn, Warrick, Eamon and Jarlath are unknown.
Landry's death in the time dilation field and Mitchell standing on the bridge.
In the same episode, Vala crying during that conversation with Daniel, even though it ended well for both of them.
Thor at the beginning. His entire race is about to die, and his one regret is his inability to help the humans more than he already has. Selfless to the end.
When Sam says goodbye to Thor for the last time, just before the Asgard hasten their impending extinction by committing mass suicide.