Angel aka Sorano Aguiera is a walking basket case with how much emphasis is put on her wanting to see her sister again. Her sob story in front of a justifiably furious Hibiki deserves a mention.
If you care about Jellal, the scene where he's apologizing profusely for Erza for what he did winds up with both characters crying by the end of it and Erza telling him that, now that she's done punching him in the face, if he buys her cake they'll call it even.
Everything to do with the relationship between Erza Knightwalker and Edolas Lelouch given the latter's brain damage and paraplegia. Poor Knightwalker.
Marianne's Death and everything leading up to it and after it until Lelouch’s departure can be seen as one of these or a massive collaboration of many.
Watching Erza go full on Berserker Tears as Morianna Feathermane reveals that she killed Erza's parents. Even in canon, Erza has never been this far gone or this enraged and in some respects, it's extremely heartbreaking.
Sindel is designed to be such a sympathetic villain that seeing her cry because it turns out that she misses Mavis, a person she saw as an older sister, might bring a tear to your eye. Hell, the resolution that she is forced into her 13-year-old self as a means of protecting everyone from her power really makes her a tragic individual.
It gets worse during Tenrou Island when Sindel gets to meet Mavis' spirit. Even the author admits to crying while writing the scene.
In chapter 100, both the scenes where Meredy and Ultear cry their eyes out when they begin their Heel–Face Turn will likely have you crying right along with them.
Undine's backstory tugs at the heart strings a little with the abrupt way her fiance is killed.
Kagura finding out that Zangetsu and Jellal are the same person. You can feel Kagura's pain escaping from the webpage and jumping out at you.
No. This one deserves a full explanation. Ahem. Jellal takes the disguise Zangetsu and meets Kagura in this disguise during the Grand Magic Games during the year X788, which is while Fairy Tail is still missing after their run in with Acnologia on Tenrou Island. Kagura has no idea that Zangetsu and Jellal are the same person, even saying to his face that she wants to kill him and not realizing she's talking to the person she wants to kill. She grows fond of him and outright falls for him over the course of a few days because he meets all her criteria towards a perfect boyfriend. And then it turns out that the very person she fell in love with is the very person she wants to kill and he is perfectly okay with that. Jellal was willing to die for Kagura both because he grew to care about her and because he wants to make up for what he did to her brother Simon. Ultear even gets in on the scene, trying to deflect blame to her given her role in the situation, but ultimately Kagura becomes resolved to kill Jellal, except she's unable to go through with it and breaks down crying because the person she met isn't the person she wanted to kill. Face it, if this was animated and put to proper music, we'd all be crying like little bitches. It's especially heartwrenching considering the build up to this scene.
This same scene is then followed up with Nivea's death, which while some might find was a dumb decision on part of draconichero, for those that were particularly attached to the character, it gets you right in the feels. There is a reason draconichero said he may as well have named the chapter I'm in an Ocean of Feels and I'm Drowning
While she wasn't around for long, many fans find that the death of Yuuki, the spirit from the immaterial plane that makes Gray a god slayer to be this.
Makarov finding out that Bob is dead. He breaks the news to Blue Pegasus and while he refuses to cry because that's what Bob would want him to do, he doesn't succeed.