Tear Jerker / The 39 Clues

Warning: Potentially unmarked spoilers!
    Series 1 
6 - In Too Deep

9 - Storm Warning
  • Amy and Natalie's brief conversation about mothers in book 9, Storm Warning. Given that Amy's mom has been dead for seven years and Natalie's mom is the Big Bad of the series who is responsible for Amy's mother's death, and psychologically abuses her children to boot, this makes for a scene that tugs at the heartstrings...especially when you see how loyal Natalie is to her mother, despite (or because of) the abuse. And how caring and big-sisterly Amy behaves towards Natalie for a moment....

    Series 2 
3 - The Dead of Night
  • When Ian thinks to himself "For that to be the price of a family's happiness? Unimaginable. In fact, he couldn't imagine a happy family at all." Made even worse by the conversation he's just had with his mother, who told him that she doesn't want anything to him or his sister, who's been kidnapped, and rubbed in his face the fact that most of the people at the Cahill Command Center barely put up with him.

5 - Trust No One
  • Alistair's death.

6 - Day of Doom
  • As if there hadn't already been enough depressing things up to this point, there is Evan and Natalie's deaths, Ian crying over the body of his little sister, and then Isabel's reaction to Natalie's death — as well as the scene where Amy sees the spirits of Isabel and Natalie walking together, holding hands, happy. It's all very sad.

http://tvtropes.org/pmwiki/pmwiki.php/TearJerker/The39Clues