In King's Ransom, Simba wakes up to find Nala missing, and feels extreme loneliness and loss because of it.
Hago physically abusing Nala, leaving her sobbing on the ground, would have to count too.
In Your Worst Nightmare, Simba is cruelly insulted by Nala and disowned by his parents. It's All Just a Dream of course, but still.
Simba manages to insult Dream Nala back, and this scene manages to be both sad and awesome at the same time.
In Miss the Girl, Simba's attempts to convince Nala that Moto is trying to fool result in a fierce argument, hurtful words from Nala, and the termination of their friendship.
Simba crying beside the tree where he and Nala met.
Simba's second attempt going wrong as well.
Hago declaring he will kill Nala first, just to break Simba's heart even more.
"I wanted to say thank you because you were the best friend I could ever hope to have, and I'm gonna miss you."
In You're Fired, Banzai's reaction to Shenzi's apparent death is a bit heart-wrenching. Subverted when she wakes up and cries, "I'm not dead, you idiot!"
In Hago's Little Puppet, the hypnotized Simba attempts to kill Nala, despite her pleas.
Two moments in Army of Evil:
Sarabi telling Simba the story of her mother's death.
Moto's death, followed by the revelation that Hago killed Muerto.
As one can probably guess by the title, Life Hurts is full of this trope. Despite the cute moments between Simba and Nala interspersed throughout, the main story focuses on Tayari, the mother of the teenage lioness Scar raped and killed in the previous story. She drives Sarabi and Sarafina away when they try to help her, and she ends up jumping from a cliff and killing herself. One can't help but think this story serves as the Very Special Episode of the series.
Tojo looking miserable in his sleep in Mtumwa Strikes Back, even though it is quickly rectified by Tama kissing him.
Nala's nightmare in Two Cubs and a Baby.
In Tama's Bet, the title character hypnotizes Simba into falling out of love with Nala, resulting in him saying some very nasty things to her.
The foreshadowing to Sick Simba in Night Terrors.
Sick Simba is filled with Tearjerkers:
The main concept of Simba dying from a painful illness is incredibly sad in and of itself.
Nala's narration throughout.
The scene where Tama finally reveals her greatest wish in life... to be loved.
The early scenes of Simba coughing, trying his best to hide it for Nala's sake.
The scene where Mufasa tells Simba that the Kulaani illness is fatal with no cure. It's even more heartbreaking because he's on the verge of tears himself.
Nala staying by Simba's side the whole time.
The scene where Nala asks Tama for information concerning the illness, only to be cruelly rebuffed by Tama.
The scenes where Sarabi and Sarafina come to say their goodbyes to Simba.
Tama sobbing in the grass, crying about how miserable her life is.
Nala leaving in tears as Simba finally starts to die.
"It's happened. I know it has. Simba is gone. As soon as he closed his eyes, I knew that was the last time I would stare into them, or stroke his cute little tuft, or have a crazy adventure with him. All the things he'd done, and it was an illness that killed him in the end. So that's how he died. That's how my Simba, the greatest cub in the world, lost his life, to the most unfair illness that someone could ever catch. His story has ended, but it will live on for ever."
Simba screaming in pain as he comes back to life.
In The Royal Reaper, it is revealed that Tojo was the prince of his pride, and that his father King Kujali destroyed the kingdom, leaving Tama and Tojo the only survivors.
Nala being tortured by the Royal Reaper would count too.
A couple moments in All Alone:
Tama breaking down in tears over her miserable life.
Simba feeling extreme loneliness after everyone vanishes.
Plenty in Goodbye, Nala:
Tama's belief that her life means nothing.
Nala tells Simba she had a nightmare where she killed him.
Tama yelling at Tojo and scratching him before running off.
The hypnotized Sarafina being so cruel to her own daughter.
In Hypnotic Glint, Simba has an argument with Nala, saying some very hurtful things before storming off into the jungle. Ironically enough, this moment leads to the sheer hilarity that fills the rest of the story.
A few things in The Return of Hago:
Simba's nightmare, which is a lot worse than the many that have come before.
Hago killing Bora.
Hago revealing that he is Nala's father.
Nala being tortured by Hago, being reduced to insanity, and then to a sobbing mess.
The opening scene of God of All, where a harsh argument between Sarabi and Simba proves to be the first sign that something is dreadfully wrong...
Towards the end of Shocker, the titular cub reveals his backstory to Nala: He lived a miserable life until he met the love of his life, but she died of an illness before she could confess her love to him.
A few moments in Darkness Falls would count:
The death of Zazu's father. He would have been killed by Ahadi, but Zazu wished for that not to happen. Death killed him instead, so Zazu bears his father's death on his conscience.Not unlike someone else in the series...
Nala's death. The text itself sums it up best: "Simba continued to sob and cry. He had lost his girlfriend. His best friend. His future queen. She was gone for ever. All her hope, all her potential, and everything she could have been was snatched away in an instant. Simba had lost the single most important person in his life."
Simba's encounter with You-Know-Who is also a Tearjerker, but in a happy way. You-Know-Who confirms that Simba is indeed what he has always sought to be: a good, honest, true soul. He even allows Simba and the other Pride Landers to be brought back to life.
The end starts as a sad Tearjerker, as the audience is initially led to believe that Nala is still dead, but it turns into a happy Tearjerker when she comes back to life and shares a romantic moment with Simba.
Zazu getting fired at the very beginning of Drought, as well as "That's what I'm here for."
In Dig It, Simba's possessed parents exile him to a camp for misguided cubs. Mufasa even drags him there by the scruff after knocking him unconscious.
Seeing Zazu in his self-pitying manner before Pori arrives. The revelation that he never actually enjoyed his job is quite saddening too.
Simba, a spunky, happy lion cub, spends most of the story being yelled at and intimidated by a harsh lion named Maana. Imagine if he really had spend 18 months in that camp as planned...
The opening scene of Shocker's Revenge has elements of this, given Elsa is a mother of three cubs, and is murdered in cold blood by Shocker.
Quickly followed by Sarafina discovering the body, with Mufasa and Sarabi coldly ignoring it.
Muerto's death in the opening flashback of The Blood Line. He doesn't even get to finish his last sentence, which would have been, "I always loved you."
The end of the story would also count, as Simba angrily quits being a hero.
Sarafina learning her daughter has mysteriously left and breaking down in tears.
Simba missing Nala throughout the story. One can truly feel his pain...
Binamu's death in Survival. Even though she was a jerk to the extreme, being impaled by a tree branch is not a pleasant way to go. Besides, she was just beginning to rebuild her connection with Haiba before dying.
In Rebirth, Haiba grieving over Binamu would most certainly count.
In Clone Wars, Clone Nala realizes she's not real, driving her to kill herself and the other clones.
The opening scene in the series in The Beginning shows Simba mourning the loss of his home and parents.
Two things in The Chase:
The reveal that Aibu murdered Ndugu and Dada's parents.
Simba sobbing as he admits to everything wrong with him in The Curse of Death.
A few things in One Bad Night:
The King of Dreams tormenting Simba.
The King of Dreams making Simba think he would be happy for all eternity, only to reveal the opposite.
Zazu's death, even though it ends up being temporary.
Plenty of moments in Tojo's Tyranny:
Tojo's argument with Tama at the beginning, quite clearly establishing that something is wrong.
Tojo attacking Tama brutally, claiming he only pretended to love her.
The revelation that Tojo will never come back.
Tojo's death, as the last thing he says is his love for Tama.
Quite a few moments in The Evil Serpent:
The opening scene with Waoga, which depicts her searching for her son Tuhuma, who was killed by Shocker a couple stories back. It's especially heart-wrenching when the narration explains what an idyllic relationship they had.
The entire subplot with Tama attempting to deal with the loss of Tojo.
Tama's stinging words to the trio: "But then we know who the real monsters are around here, don't we?"
In The Lost World, Haiba actually begins to cry when he realizes he's being blackmailed by Tama. Hearing her chuckle evilly doesn't help.
Nala's reaction to Simba's behavior: "What's the point of loving someone who doesn't love me back?"
Seeing the dinosaurs chained up by The Hunters.
And most infamously, Haiba killing Tama at the very end.
In the follow-up, Haiba's Wish, the first chapter consists of Haiba hiding in a dark cave while a vicious rainstorm pours, constantly reminding himself of what he did to Tama at the end of the last story.
Haiba learning that everyone in the Grand Lands save Amri has died. It's even worse when you consider Amri herself. She's been living alone for ages, believing her son to be dead.
The scene with Tama's grave in Return to Camp Kazi.
Nala comparing Simba to Scar, and Simba furiously denying it with a line similar to one of Scar's in the film.
Kambi not being able to escape the camp.
None of these even compare to Haiba's death in The End:
Haiba: Simba... I'm sorry. About Tama. About everything... I messed it up. Simba: No. It's not your fault. It's mine (Looks at scars he gave Haiba.) I shouldn't have hurt you like that. Haiba (crying): It's okay. You're my friend, Simba. I forgive you. Simba (also crying): I don't hate you, Haiba. You're my friend, too. Haiba: Thank you. (Haiba dies.)