Ed and Al's backstory and how badly their attempt at Human Transmutation goes. Ed loses his leg and Al loses his body and Ed is screaming in pain and wracked with guilt. He then uses his blood to craft a Blood Seal to anchor Al's soul to a suit of armor, which costs him his arm. Al manages to get him to Winry's house and begs them for help. Shortly afterwards, Mustang and Hawkeye visit the area and find out what happened and upon meeting Ed, grabs him by the shirt and demands an explaination about what happened while he's in a Heroic B.S.O.D., complete with Dull Eyes of Unhappiness. Al ends up doing nothing but apologizing the entire time.
Nina's tragic death on top of turning into a Chimera. The moment you realize that an adorable 5 year old girl has been horribly, painfully, and forcibly transmuted, into an unholy abomination by her father no less is horrific to say the least. Not to mention the fact the reason why Tucker did this to his daughter and dog. Simply because. No grand scheme or grab for power. Simply because. The fans were practically begging Ed to hand Tucker his ass.
In both the first anime and Brotherhood, Ed actually does start beating the man, only for Chimera/Nina to grab his coat and plead with him not to hurt her daddy. *shivers*
It rocked them to the core. Even in the ending, Ed and Al didn't forget this...event.
Ed: We can't even do anything to save one innocent little girl... so what good are we then?
Scar then kills both of the Tuckers, one in an act of justice, and the other as an act of mercy. Afterwards he steps out into the rain, and prays for both of them.
The aftermath of Scar's attack on the Elrics ends with Al damaged and unable to move, and Ed, losing his will to live after what happened to Nina. He was going to let Scar kill him as long as he left Alphonse alone. After Al yells at him for not running and for stupidly thinking that dying will solve anything, Ed just quietly says "We're a pathetic pair, aren't we brother?".
Basically any time Armstrong cries for real. Whenever this happens, the fans are usually crying alongside him.
The entire flashback about the war in Ishval is a Tear Jerker marathon that lasts a whole collected volume of the manga. Also, Ed digging up the body they transmuted when trying to bring back their mother to see if it was really her, and Hohopapa's Manly Tears when Ed tells him his mother's last words.
It wasn't the Hughes' funeral itself which was so profoundly impacting. What really brings everyone to tears is poor little Elysia:
This scene is even more tragic in Brotherhood, as you can hear the sheer despair much more clearly.
Elysia: Daddy said he has important work he needs to do! No, stop it! Stop putting dirt on him! DADDY!!!
In the manga, during Elysia's outcry, even the Fuhrer is unable to keep his composure, with his hands shaking on his sword's pommel. And considering who he is (on so many levels), this is especially emotional. However, it's later revealed he was shaking for a different, much less sympathetic reason...
Armstrong trying and failing to keep from weeping at the funeral can be quite jarring, if only because it's one of the few times in the series where his shedding of tears isn't played for laughs.
There was also Roy claiming to be going over formulas for human transmutation, and that he understood what drove the Elrics to try and bring their mother back.
As pointed out on the main page, the above doubles as a brilliant metaphor; Roy is powerless in the rain, and that is how he felt at that moment.
Episode 16 of Brotherhood has another one from the poor kid, possibly the most upsetting in an episode filled with these.
Elysia: *opens the door* Papa! ... *runs into Winry's arms, sobbing*
Also continues in the manga, where after Ed asking Gracia's (Hughes' wife) forgiveness for involving (and indirectly causing the death of) Hughes in their trouble. Gracia's response is to assure them to continue and not to let her husband death be in vain. All with a motherly smile and strong composure. Then they leave their house, and Ed just looks back for the last moment, through the window, seeing Gracia crying with Elicia in her arms.
Ed:...It would've been easier if we got scolded.
In Brotherhood, Hughes' death itself is even worse. We see Hughesstruggling to reach the phone after getting shot, failing, and saying his last words:
Hughes: Gracia... I'm sorry. Elicia... never forget... Daddy loves you.
The flashback in episode 12 to Izumi's attempt at Human Transmutation. Especially the soundtrack, and her screams when she looks up at sees what she made...
Then, Edward and Al try to act nonchalant about what happened to them... and just when you think she'll hit them, she actually embraces them and tells them that they can stop pretending. They embrace her as well and just break down apologizing.
Lan Fan cutting off her arm is pretty shocking, but the first time she looks in the mirror afterwards is devastating.
Her grandfather Fu's reaction is bad too. At first he's absolutely furious that she failed to protect Ling and is on the verge of hitting her, and does slap her across the face in Brotherhood. Then Dr. Knox draws his attention to the fact that she's missing something, Fu's voice tone and body language completely change from anger to dejection and denial, murmuring " her arm, it's... it's not there..." in utter horror, and he falls completely flat, crying. The manga keeps the scolding, but Fu gradually breaks down in tone, ending on the verge of tears on "You don't even have your arm anymore..."
The time when Ed convinced Winry not to kill Scar in Episode 22 by saying: "With these hands, you delivered a baby. You saved his life, and his mother's. With these hands, you gave me an arm and leg to stand with. These hands aren't meant to take lives, but save them." A Tear Jerker, an Awesome Moment and Crowning Moment of Heartwarming at the same time, because Hiromu Arakawa is just that brilliant.
Made worse as the ending song starts and you hear "let it all out".
Poor Armstrong, To see him, the strongest and most muscular character in the manga bawling his eyes out over the body of a dead Ishvallan child.
The first 19 or so pages of Chapter 68 of the manga: Hohenheim leaves the family, to counteract Father's plan to kill everyone in his country. While gone, his wife dies and his eldest hates him for leaving.
The photo... Just, the photo, ever wonder the reason that Hohenheim's face is covered in the photo? It's because he's crying, after Trisha told him that she did and always will love him.
The author's note at the opening of volume 15 talks about Arakawa's research into the subject matter to be covered by the volume.
In researching this volume, I interviewed veterans who had been on the front during World War II. I read countless books, examined film footage, and listened to many detailed and intense stories firsthand, but the comment that affected me the most came from a former soldier who lowered his gaze to the tabletop and said "I never watch war movies."
The Brotherhood rendition of Scar's backstory, which takes up a good part of the aforementioned episode 22, is no less heartbreaking. It's specially poignant because the flashback is almost all in black and white, save for the blue eyes of both cold / evil and good Amestrians as the Ishvalan massacre takes place...
A Tear Jerker of happiness this time: Ross, having revealed to have faked her death, orchestrated by Roy, who, as it initially appeared, had murdered her. It is staged so that the reader/viewer is out of the know that she is still alive until Ed and Armstrong arrive in the ruins of Xerxes, and Armstrong's overflowing tears of joy bring the viewer with him. Just the fact that Roy once again proves why he is such a fan favorite, that he did not suddenly become an arrogant traitor, and that such a relief can exist amongst a very depressing part of the story with many deaths...
However, there's a scene before that one that was far from happy or heartwarming. Just after Mustang had faked Ross' death, everyone is gathered around for an autopsy report, during which Dr. Knox reveals that the charred corpse is in fact Ross. After the fact, Armstrong approaches Mustang, and deeply apologizes for her actions since she was one of his men...and visibly shaking, as he is clearly upset. However, what truly makes the scene (particularly in the anime version) is when the camera slowly pans upwards, and reveals the look of barely-contained rage on Armstrong's face. He clearly wanted to beat Mustang to death right then and there, and it was taking every ounce of willpower he could muster to hold himself back.
Chapter 94, Hawkeye to Mustang talking him down from killing Envy and threatening to shoot him herself:
Mustang: What will you do after I'm dead?
Hawkeye: I have no intention of living on alone. After this battle is over I will erase my life, along with the secret to flame alchemy that's led good men to madness.
Roy's statement afterwards adds to it:
Mustang: That won't do. I can't lose you.
Speaking of Mustang and Hawkeye, what about Research Laboratory 3, when she thought Roy had been killed by Lust? It's simply heartbreaking to see such a normally stoic character completely break down, with tears streaming down her face, and it's strongly implied that if Al hadn't been there, Riza would have let herself be killed as well.
Al's reason for wanting to get his body back.
Al: I don't want to be alone at night anymore!
The lead-up to it is pretty heartwrenching as well, as the brothers and Izumi realize that they didn't end up killing the people they were trying to revive a second time.
Al referencing his inability to cry when talking to Winry. He discusses how Edward doesn't take the chance to cry, when he's lucky that he has tear ducts.
Remember that scene early on in the series, with Ed and Al sitting in the rain, and Al talking about how he can't even feel it? He wasn't even complaining or anything, just stating the truth.
Havoc's breakdown after losing the use of his legs. Sure, he became a full-fledged Handicapped Badass later, but that scene where he's begging Roy to just give up on him and cut him loose from the plans is crushing.
Even the previous hospital scene, when he reveals that he can't use his legs anymore, is a tearjerker as well.
Ling's breakdown after that was already heartbreaking in the manga, but Brotherhood just made it even worse, if that's possible. Maybe it's being able to actually hear Ling's screams and watch tears visibly stream down his face, but the whole scene in episode 58 with Ling desperately crying out for someone to use his stone to save Fu, only to get a cruel realization that despite the powers he's obtained he can't do anything for the situation is heartwrenching.
Ling: Why...?.... I've finally gained immortality, and I CAN'T SAVE EVEN ONE OF MY SUBJECTS!? DAMN IT!!!!
Ed pleading with the Truth after realizing Al was taken away. "Give him back! He's my brother! Take my leg! Take my arm! TAKE MY HEART! ANYTHING! YOU CAN HAVE IT! Just give him back! HE'S MY LITTLE BROTHER, HE'S ALL I HAVE LEFT!"
Points for Vic Mignona for perfecting the sheer desperation, rage, and terror in Ed's voice.
Lieutenant Hawkeye getting a sabre to the jugular.
Olivier's reaction, or better yet, lack of reaction to Buccaneer's death. The other character's faces show it itbest.
The ending of the episode of the Brotherhood OVA "The Blind Alchemist". Edward and Alphonse find out that the blind alchemist's human transmutation of little Rosalie was in fact a failure, and that everyone in the mansion is deceiving him to keep him from knowing the awful truth. Hence, his attempts to bring back a dead loved one resulted in a near-lifeless husk, an orphan pretending to be Rosalie to lead the deception along, and the loss of his eyes as "payment."
Alphonse: "They're all good people."
Edward: "Yeah. But... nobody was saved."
It may be an omake, but it nevertheless turns to Fridge Horror due to a later realization in the series: the dead are impossible to bring back to life. Whatever it is lying in that bed, it is not Rosalie.
That particular omake was originally a side comic featured in one of the extra books for the series. The original version of Ed's line is much more ominous.
Whatever's in Al's body: Don't you want your real body back?
Al: Of course I do! Always! Always for years and years! I've dreamed about getting my real body back! But... but!! I... can't... I can't have that body... not now...
Many people cried when Roy lost his eyesight. The poor guy just doesn't get a break.
Roy:: I...can't see...
Hohenheim's flashback to when he leaves his family, describing his life to Trisha.
"In the years since I got this body I've seen a lot of death. I tried to think about it as part of the great cycle, and that made it easier somehow… and every time I see something wondrous I believe it was worth it, that I stayed alive all these years. And then I met you, and together we created two sons. I don't age, and yet I see my sons grow up before my eyes. And suddenly I'm terrified…"
Chapter 104. Seeing the nation wide circle being activated and watching the world start to die...especially the scene where Winry collapses.
Seeing a mountain of strength and exuberance like Armstrong dead and motionless on the ground reaches a whole new level of wrongness.
Also in episode 41 of the anime, the part where Ed gets Heinkel to remove the metal beam from his chest and then attempts to use alchemy to seal the wound using his own life force instead of a philosopher's stone.
Bradley's last words. Makes you almost forget that he's a hateful, genocidal bastard.
"I didn't believe in God, or something like that, but this must be what they meant when they said, 'God has forsaken me', isn't it?"
"Remember who I am. I chose her (his wife)."
"Thanks to you humans... my life... had been a good life.... A life worth living for. And... maybe even... a life... worth... dying... for..."
Al, still suffering from a Heroic B.S.O.D. from his fight against Barry, confronts Ed and demands to know if he's real or artificial, stating how easy it would be to fake a construct's memories, and pointing out how Ed was reluctant to ask him something. Cue Winry smacking Al with a wrench, and telling him, tears welling in her eyes:
"You know what he was so afraid to talk to you about? HE WANTS TO KNOW IF YOU BLAME HIM FOR WHAT HAPPENED TO YOUR BODY, AL!!"
Also Ed's just slamming his hands on the table and just quietly saying "Is that what you think.." and walking out quietly, completely dejected by the accusation.
And then the flashback happens of Ed rambling endlessly about how guilty he feels and how it's all his fault and that he's terrified of Al hating him.
At one point during that fight, Envy looks at Roy with an expression that can only be described as sheer terror. The sadistic little palm tree clearly didn't want to see what was in store for him at that point, and it manages to make him almost pitiful. He even seems to whimper a little.
If the above has no effect, then thinking of its effects on Roy Mustang may change it. Roy's biggest desire, which Hughes shares, is to change Amestris' society so peace will be achieved and nothing ever similar to the Ishvalan Massacre will happen again. Here, however, by beating and burning Envy pretty much to death, Roy is his Darkest Hour... and about to completely betray these noble ideas and dreams. He's about to become the very personhe detests the most, out of trying to avenge his best friend's death. It's a damn relief to see Ed and Riza appear and manage to snap the guy out of it.
When Pride thinks of his "family" when Ed takes over him. And when he's been reduced to his true form, and we see him cry for his "mama".
It's a little hard to feel sorry for Pride, but the look on Mrs. Bradley's face when Ed hands him to her in the penultimate episode. Especially given that we've watched her being manipulated by Team Mustang for the past few episodes. Just imagine how devastated she must have been to learn that the family she loved so much was a lie and that her concern for them had been exploited for the gain of the revolution. Ouch.
Chapter 107: Al uses his body to shield May from Father's attack, getting nearly destroyed from it, a crack just millimeters from his bloodseal. Then, when Ed's automail arm is destroyed and he's pinned down with Father about to kill him, Al (with the help of May) sacrifices his soul to restore Ed's real arm. May's tears as she sets up the arrays and Ed's look when he realizes what Al is doing are just heartbreaking.
Ed's reaction to the above: three words.
Ed:"YOU STUPID IDIOT!!"
The Funimation dub version of the above, where Vic's voice breaks.
Ed:"AL, YOU DUMBASS!!!!!"
Another scene from 107 when Al is finally reunited with his body at the Gate and confronted by the Truth.
Brotherhood's fifth opening, appropriately titled "Rain" — seeing King Bradley possibly crying and the overall tone of the song can certainly inspire such moments.
That opening also includes a scene foreshadowing Roy losing his eyesight. Seeing that pillar of strength and rebellious spirit looking so incredibly broken◊ is almost too much to bear. Not helped at all by the fact that it's immediately followed by Riza holding Black Hayate and crying.
How about the ending "Let It All Out" by Miho Fukuhara? The song has a very sentimental tone...
What makes it worse is that Ling accepts that they will have to make the sacrifice to save the others and asks Greed if he'll stick with him to the end. Greed agrees and Ling smiles, then Ling discovers that Greed tricked him. His breakdown into tears and sobbing is understandable.
Also, "That was my first and last lie."
A nod to the English voice acting as well: try not to feel just a little bit heartbroken at how devastated Ling sounds when Father is destroying Greed.
Hohenheim offers his last human soul, his own, for Ed to use to bring Alphonse back. When Ed demands why, Hohenheim responds with the fact of his fatherly duty before admitting that much of the grief he caused to his sons was because of him leaving before asking to be let to do this one last thing.
Ed is stunned before he refuses it vehemently all while finally calling him father. And for the first time in the series, heck probaly since the accident, Ed was crying. It shows a strong moment of vulnerability and just how much Hohenheim leaving impacted them. Hoenheim even apologized when he saw his son's tears.
Hohenheim returns to Resembool and dies next to Trisha's grave with a smile on his face. Pinako finds him:
Pinako:"Hohenheim!... You idiot... Dying with a smile on your face...
Brotherhood makes it even better by dedicating the ending credits to him in episode 63 right after he dies.
"Alphonse! Someday, I swear I'll come back for you. Just you wait! Just you wait!"
The new OVA "Yet Another Man's Battlefield". It features eighteen-year-old Roy at the military academy, meeting Hughes (whose appearance in itself might reduce someone to tears given what happens to him...), and befriending a fellow Ishvalan trainee named Heathcliff, after standing up to some bullies. See where this is going? Years later, the Ishval War of Extermination happens. In a nutshell, Roy, now the Flame Alchemist, meets Heathcliff again, who is clearly in despair over the murders of his people. He shoots Roy, before being shot himself by Hughes. The scene then skips to the manga omake where Roy asks Hughes about what he has to live for. And of course, "...Give me 30 seconds." Seriously heartbreaking...
The words on the next-to-last pages:
A lesson without pain is meaningless. For you cannot gain something without sacrificing something else in return. But once you have overcome it and made it your own...you will gain an irreplaceable Fullmetal Heart.
Combined with pictures of everyone with their happy endings.
Reaching the last page of the final chapter and realizing one of the greatest manga in existence is finally over.
The true tearjerker is a good one-where the readers are thanked for their support and love.
In Brotherhood, when discussing the sheer brutality of the Ishval massacre, we are often shown a giant wall being alchemically formed before a group of Ishvalans running desparately for their lives, and then they get gunned down by the soldiers chasing them. In the full on flashback given by Hawkeye, we see that the one who made the wall was Armstrong! The look on his face as he hears the gunshots is just...devastating.
Even WORSE in the manga. Armstrong goes to the other side of the wall to see what happened and is walking in a complete daze among the dead bodies. He comes across an Ishvalan woman and her mother, who survived the massacre by hiding in a crevice the whole time. To alleviate his conscience, he busts a hole in the wall he created and tells them to flee. He watches them run off only to see them get blown to bits by Kimblee, who observed the entire scene and was, worse yet, trying to help Armstrong dodge a court-martial. Cue Armstrong dropping to his knees in shock.
Seeing Basque Grand trying to spare Ishval can also be quite sad when you know that all of his efforts are going to fail, Bradley is going to order the genocide to continue, and that in the end, Grand is going to be killed by one of the Ishvalan survivors.
"I curse you". It's a small line from the last Ishvalan killed in the war, but it's incredibly powerful because he doesn't look angry at Mustang. No, he's quietly stating that Roy will carry the demons of Ishval for the rest of his life. And Roy can't do anything but look at him in the eye as he executes him.
The discovery that the Elrics didn't even manage to bring back their mother. Ed goes into a minor breakdown about it, followed by Izumi crying in relief that she didn't kill her baby a second time.
The look on Greed's face when he admits, in his entire life, that all he's ever wanted was friends. Especially poignant in the anime where we see his eyes shimmer a little, as if saying if he wasn't who he was, he'd cry from this revelation.
Ling: Greed, this is what you desperately wanted, isn't it?
Greed: Yeah, you're right.... This is what I wanted. I wanted the chance to have friends like these.
When Izumi finds out about Al and Ed's attempting Human Transmutation in episode 12 of Brotherhood, after explaining what happened to her and sympathises with them, she tells them it's ok to let themselves hurt. Cue her hugging them both as Ed and Al break down apologising and begging her to forgive them.
What's really sad is when you examine the Homunculi, creatures formed from Father's emotions and desires, and realize that what Father really wanted was that same love and support that wound up defeating him, a desire so deeply buried and denied that neither he nor his children (save Greed and Envy, and Envy committed suicide out of shame for it) were ever able to admit it. To really rub salt in the wound had he from the start simply asked Van Hohenheim, his own "father" whom he freed from slavery and who was fond of him (before the whole, y'know, genocide of Hohenheim's people thing, Hohenheim would have given that love and support to him in a heartbeat.
Well Bradley... my soldier was strong... wasn't he?
Lust's death was a Crowning Moment of Awesome for Roy, but Gluttony and Envy's reactions to it were this. Gluttony is sitting there on the floor, crying and moaning out Lust's name, while Envy is completely furious at Wrath for letting Roy get away with it. It just seems to show that, for all the Homunculi are, they do seem to care about each other.
A rare example of a Fridge Brilliance form of tearjerker can be seen when you compare what each of those who preformed human transmutation lost.
Ed who was almost completely independent and strong willed as a child lost his leg, and his ability to stand on his own.
And another gut punch for him, if you think about it, was losing Alphonse. It was Ed's idea to try to bring their mother back through alchemy, to keep their family together. So by taking Al, the Truth took away the only family Ed had left.
Especially when you see what Truth took in exchange for Al's soul, his right arm. This signifies the Lancer role and the right-hand man nature Al is to his brother.
Al who praised family and relations more then anyone lost his entire body, trapping him into loneliness at night and robbing him of the ability to ever feel his mother's warmth again.
Izumi in trying to bring back the child she had lost, lost the ability to ever have one of her own.
And lastly Roy, who spent the latter part of his life attempting to build a better future, lost the ability to see what his vision would create.
Even at the very end, Ed and Al never forgot Nina◊.
Even Barry the Chopper gets one when he rejects the idea of rejoining his human body, noting that it was rotting and "won't last much longer". When his body (inhabited by an animal's soul) scratches his blood seal, he smiles as he truly dies.
Gluttony's terrified reaction when Pride betrays him and eats him alive. To make matters worse, his last words are him screaming out for Lust.
Ed's utter howl of misery at the end of "Night of the Chimera's Cry", both for the original Japanese and the English dub.
In the dub, at least, Vic really sells it. His pained sobs sound way, way too real for him to just be acting.
How the chimera keeps asking Al if they can play. Each time it asks it gets worse.
In the first anime when Tucker snaps and uses Al's Philosopher's Stone body to try to bring Nina back.
A bit of Fridge Horror made this even worse. Because her father promised Nina to play with her the next day, it all might have made perfect sense to her. She and her dog sitting in circles drawn with chalk, her Dad being all excited... Bloody Hell, she probably thought her father would be showing magic tricks to her till the very end.
The Mercy Kill. Y'see, in Brotherhood, we meet Chimeras who, while rather unhappy with their lot, are relatively well-adjusted and even looking into ways to restore themselves. If there was anything, anything at all, that could've been done to help Nina in the slightest, well... That door was slammed shut.
Oh God, Roy's flashback in episode 13. If the lighting, the hesitation of both characters, and "Regret" playing in the background wasn't enough, then Roy's shadow on the wall flaring up as Roy incinerates the poor boy absolutely killed me.
Episode 27, near the end. Izumi has just beaten the living crap out of Ed and Al after they finally confessed to attempting to bring their mother back. She stands before them, angry and disappointed. Then she walks over and holds them close to her. Cue a piano rendition of "Brothers." Both Ed and Al begin to cry. Gaaaah. Such a simply crafted scene, but easily one of the most powerful and beautiful in the entire series.
When Izumi explained the concept of death to one of the children who regularly came by after her cat had died.
More or less anything to do with the first anime. Wrath, who is not so much evil as deeply, deeply unhinged for understandable reasons. The demise of his surrogate-mother Sloth itself fairly teary, is a particularly good example of this, with Wrath inadvertently helping Ed to kill her and breaking down into full, honest-to-god tears afterwards. Imagine a horribly twisted 12-year old bawling his eyes out as his "mother" slowly dies in front of him/in him.
Don't forget "Reunion of the Fallen". Half Tear Jerker, half terrifying.
One that really got to me was Greed's death, especially because of how much it comes across as essentially suicide, particularly with his inspirational speech of the dire need to stop his fellow Homunculi. It's also amazing to see Ed try and succeed in killing him one second and then start crying and screaming for him to wake up when he realizes the full import of what's happened.
You think that dub scene was bad... episode 8 anyone? This plays out in a shorter form after the Nina revelation in the manga and Brotherhood, but the first anime is a whole lot more powerful as this was after a near death experience.
Ed: When I was certain he was going to kill me, my mind went blank, and I didn't have any hope anymore. And the only thing I could do was scream my lungs out. I felt so helpless, I couldn't even bring myself to believe someone might save me. Then you showed up, Al. And I realized that if we don't take care of each other, then no one else will. So I'll do anything in my power to get our bodies back, even if it means being the military's lapdog. And we'll just have to hope our powers are good enough to help us rise above our own limits. [cries into his hands] 'Cause we're not gods. We're humans. Tiny, insignificant humans...who couldn't even save a little girl...
Heck, the last minute or so of the second-to-last episode of the first anime was a combination of sadness and "What just happened" due to the rapid series of events. One heart-wrenching word: EDWAAAAAAARD!
No mention of the episode we see Ed and Al's past? The song Bratja at the end really hits it home, even if you don't know Russian.
Speaking of Bratja, Vic Mignogna's now famous cover of the song. After a while, you stop seeing it as just an English cover that happens to be sung by the protagonist's voice actor...eventually, you come to see it as the real Edward Elric, singing his regrets to his brother and pleading for his forgiveness.
While in Lab 5, the Slicer Brothers beg Ed to kill them, but he refuses, since denying they were human would mean Al was no longer human either. As this exchange is going on, Barry is convincing Al he's not human, only a product of false memories. If Ed's heartfelt speech isn't enough, the background song, Bratya really pushes it over the edge.
The entire subplot of Tucker trying to bring back Nina. Yes, he's a sick, amoral monster deserving of punishment. But as the show progresses, it's clear there's a side of him that truly loved Nina and wanted her back, but to no avail. By his last appearance, he's only left with a soul-less "doll" of her, and is so insane at this point that he doesn't know this. The mere idea of ANYONE being that messed up is just too much.
And don't forget Maes' funeral. Everyone's sad enough, including the viewers, even if we hadn't seen the funeral scene, to top it all off, his three year old daughter, who doesn't understand the concept of death and cries, asking why they're burying her daddy.
Fridge Horror when you realize that they accidentally broke Hughes' family the same way Hohenhiem did to their family.
Not to forget, that the words of Elicia even make the mega-badass Alex Louis Armstrong cry... Which is probably not so unexpected, because he had a mental breakdown, seeing the horrors of the Ishval extermination war, making him unfit to continue. And he tends to be especially touched by those kind of displays of affection, although it was mostly Played for Laughs before that.
Lust's death. She starts out as a monster. But seeing her go completely soul-crushingly depressed after Scar's death was just too much. After his death she never even smiles after that. She solemnly agrees with everyone after that. Even the Elrics that say they can kill her. And then when she teams up to kill Sloth she looks so sympathetic, and to top it off, as Wrath kills her she agrees with him on some level.
Gluttony's reaction to it. He had pretty much been established as brainless and completely amoral. Seeing him break down over her death and constantly asking where she is, although nothing compared to most of the other examples on the page, still tugs at the heart-strings slightly.
After Ed tells him that Lust is dead, the poor little guy just flops onto the ground and loses the motivation to do anything besides sit there and mumble her name. He's so far over the Despair Event Horizon, that the only way he manages to get out of it is for Dante to basically erase his brain. And even then it's implied that it wasn't entirely effective, as in the movie Gluttony goes on a Roaring Rampage of Revenge against Wrath (Lust's killer) and completely ignores Al.
Scar's final conversation with Lust. He points out that he loved her human form but also hated his brother for learning the forbidden arts of alchemy to try to bring her back. And yet the love that the Elric brothers felt for each other made him realize that he loved his brother.
The opening theme of Conqueror of Shambala, it may be one of the few good things about the movie, but the opening theme play a somewhat melancholy, yet upbeat song and show clips on what happen through out some of the 51 episodes. It also includes some of the most very sad moments like Hughes's death or Chimera Nina or Scar shedding a tear. Just check it out
Anything about Izumi in the movie. Her dying is a shocker, especially in hindsight for manga fans. But her being reunited with her son in death... Sob.
The airplane scene broke my heart with Edward slowly making his resolve, turning away, then his heartwrenching calm voice as he explains himself to his brother, the way his face quivers for a moment... and THEN Al starts screaming and crying.
And then the cut to Winry who calmly states that Edward now never again will let her wait - and then her face quivers. This broke my heart the second time.
Alfons. Anything about Alfons. Starting with his life, continuing with his relationship to Edward who only sees a shadow of Al in him and doesn't even notice how much he hurts him that way ending with his Heroic Sacrifice. That man deserves a seat of honor here.
Rick and Rio's scenario. One of them hates their mother for "forsaking" them, when it turns out she was basically blind and went out to see them but ended up dying looking for them.
Selim's death. In this version, he's not Pride, but an innocent kid. And killed by his own FATHER at that. And then there's Roy Mustang carrying the little body away from the house after going on a fiery revenge.
Rose. Being raped, manipulated, made mute, and generally all the crap she went through. She didn't have it good in her first appearance either.
There's something bittersweet about episode 4. Majhal was so in love with a woman who died that he tried to bring her back to life, and obviously failed. He essentially murdered several woman in attempts to bind their souls to mannequins that resemble his lost love but they never bind correctly. At the end of the episode it turns out "Lebi", a woman who often visited Majhal, was his supposedly dead lover - Karin. Majhal refused to believe that the woman was Karin -as she was now older than before and no longer "beautiful" to him - and tried to attack her but he accidentally became impaled by his own sword. Even while dying Majhal refused to acknowledge that Lebi was Karin, and that she was alive.
The dejected look on her face as Majhal, with his dying breath, flat-out rejects her (and over something as shallow as aging) makes it even worse.
Sloth's death - when she's evaporating after Ed transmutes her body into alcohol, it's possible she remembers who she once was as she says her last words. And the look on Ed's face!
Nicely done, sweetheart. Clean up after yourselves, and take care of each other.
The Lab 5 scene, where Lust threatens to rub off the blood seal in Al's armor unless Ed makes a Philosophers Stone for the homunculi, and Ed pleading her not to.
Al having Martel killed while she was inside of him. Her blood is gushing out through the gaps in his armor and he just kind of sits there sobbing that he couldn't save her when he tried so hard. To make it worse, it's the only time in the 03 series that armor Al cries onscreen. It really hits home that he's just a vulnerable kid trying to be cheerful for his brother's sake, and that for all the times we see Ed crying onscreen, Al is probably crying too, silently.
Barry the Chopper is Nightmare Fuel incarnate. The scenes afterwards are some of the most depressing in the series. Narrowly escaping death, and still mourning Nina and Alexander, Edward's in a state of agony. To make it worse he's only twelve and has had so much happen already. His speech, stated above, drives it all in but Alphonse isn't much better.
Al: Since I no longer have a mortal shell, I can't feel the terror you felt, thinking you were going to die. I'm sure it must have been painful, and lonely. I want my body back, brother. I want to be able to feel what you felt. To feel human again. If we find the Philosopher's Stone, I can have that.
During episode 6, while Ed is taking his exam:
Alphonse: I don't know if we chose the right path, brother. But I do know this: I don't want to be in this suit anymore. I want to feel things again. It's strange. We've been right beside each other all this time. But I can't remember what your skin feels like, or how you smell.
When Edward sees the corpse of a woman who was killed by Barry he gets triggered by memories of his mother and that... thing... he and Al created, and passes out. Shou says the entire time Ed was asleep he was crying to his mom that he was sorry. The look on his face... Oh, God, that horrified look of fear and sadness and pain... it's just heartbreaking.
Before that, said woman's son can be seen clinging to the sheet she's under and crying. When a soldier tries to pull him away, he gets hysterical and begs them not to take him away from her. The clincher? The poor boy couldn't be much older than five.
Ed and Mustang's farewell in Episode 48, as Mustang goes off to confront the Fuhrer and Ed to find Dante, is especially poignant given Ed's previous antagonism-cum-hatred towards his superior. Mustang goes to salute, then smiles a bit and offers his hand instead - Ed slaps his fingers, and smiles back. There's an air of finality about it that says neither expects to see the other again.
Many, though everyone remembers the deaths of Maes Hughes, and Nina/Alexander.
There's also the last episode where Al sacrifices himself to resurrect Ed, and restore his body. Afterwards, Ed sacrifices his new arm and leg to save Al from death.
Al:This is for you brother. I'll miss you.
"Edward ... why does it hurt here?"
The ending of the first video game where Armony and her father die, while Ed and Al are helpless to do anything about it.