This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Artemis Fowl
Artemis's situation in the first book is quite distressing from an objective point of view - his mother is mentally addled from grief and refuses to leave her attic room, his father is missing and presumed dead, and he's virtually alone in a house with no one but his bodyguards for company.
The part where he goes into his (insane) mother's bedroom and she doesn't recognize him only gets sadder as you age.
Butler's death in The Eternity Code. His instinct is to throw himself between Artemis and the threat. The heartbreaking part is Artemis is so much more than just a job to him - as Butler dies, he tells Artemis his first name. The scene only gets sadder when you look at Artemis, who's crying and thinking about how they were supposed to die together.
Commander Root's death in The Opal Deception. Simply everything in that chapter.
Likewise, Holly's reaction when she believes Artemis and Butler have been bio-bombed.
Holly saying goodbye to Commander Root in The Time Paradox because she never got a chance to during The Opal Deception.
The entire chapter of The Last Guardianwhere Artemis is about to sacrifice himself to stop Opal opening the second lock, and he reflects on how he has matured and how 11-year-old Artemis would never have dreamt of risking his life like this. Then Holly tries to sedate him to go in his place...
Most particularly, when Butler catches Artemis (who, need I remind you, has been his sole purpose for god-knows-how-long and who he cares for very much and would do anything to protect) and Artemis is already dead.
These lines from the same book:
Holly: "Please don't hate me forever, Artie. I couldn't bear that."
Artemis: "I was a broken boy and you fixed me. Thank you."