Adam talking to the young boy with OCD who killed his dad.
Angell's death and Flack's reaction to it.
The entire episode "Indelible". It was a Sept.11th 10th anniversary tribute, which should clue you in.
The pilot, 'Blink', when Mac goes to Ground Zero.
"Run Silent Run Deep", the scene where Danny breaks down in Mac's arms after his brother is beaten for wearing a wire.
"Flash Pop", the lab techs' tribute/vigil for their colleague who was murdered at the beginning of the episode.
Every bit of Mac's time with Claire in "Near Death". Just try watching that without a box of kleenex.
The episode about sex trafficking. One of the victimized girls managed to get a postcard back to her father in the Ukraine begging for help, and he came to look for her. Unfortunately, he ran into the exact wrong person to show her picture and ended up stabbed to death to keep him from interfering. When the poor girl is rescued and brought to identify his body, she completely breaks down and can only cry and repeat "I love you, I'm safe".
The last scene of "Command+P". Just...wow.
"Battle Scars", when the motive and plan for the murder is revealed. It was a tragic accident precipitated by the victim's insecurities and not realizing that even fake bullets can still kill.
The third episode of the first season, American Dreamers. The kid was obviously very talented; yet no one knows who he is, and worse no family comes to claim the bodywhich means that despite the forensic drawing of the guy he either has no family, or his family doesn't want to claim him.