This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Star Trek: Enterprise
The alternate version of the 31st century seen in the "Shockwave" two-parter.
Animal lovers can cry at Porthos getting sick in "A Night In Sickbay."
Travis learning of his father's death in "Horizon." Especially since the two never reconciled after Trav left the Horizon to join Starfleet.
The final scene of Season 2's "Cogenitor." The episode itself is arguably one of the most powerful Star Trek fans had seen in a long time, and the shockingly tragic Twist Ending ensures that status. (And it was written by the often-derided Berman and Braga, to boot!)
Trip's Story Arc in Season 3 as he attempts to ignore the death of his little sister in the Xindi attack, culminating in "The Forgotten" when he finally breaks down and admits to himself that Elizabeth is gone.
Tucker: Crewman Taylor had a real knack for this kind of thing. But Taylor's not here, is she? And neither is Crewman Kamata, or Ensign Marcel, or a dozen others. [...] We found Taylor over there, outside her quarters. She was probably trying to get to her station. If she'd made it a few more meters, I wouldn't be trying to write this damn letter. 'Cause every time I start, I hear myself saying what a fine young woman she was, how smart and full of potential. And I realize that I'm not thinking about Taylor at all. I'm thinking about Elizabeth. There's so many people dead. I tried not to see her any differently than the other seven million, so I've spent the last nine months trying to pretend she was just another victim. But she's my sister, T'Pol. My baby sister. (cries)
And his letter to Taylor's parents:
Tucker: Mister and Mrs. Taylor, by the time you get this, Starfleet will have already told you about Jane. Since I worked so closely with her, I wanted to add my personal condolences. I have to confess, I've been putting off writing this for a while. I convinced myself that my duties on Enterprise took precedence. But the truth is I didn't want to face the fact that someone so young, with so much promise, could just be gone. But I'm facing it now, and I find myself thinking how important she was to me. She was a great engineer, and she was my friend. She won't be forgotten. (puts down the photo of his sister) Goodbye, Elizabeth.
Major Hayes dying in "Countdown" and Reed trying to comfort him, then having to go and tell the rest of the MAC Os what happened.
Especially since, for the first two seasons, the only way Reed could open up to people was with the threat of impending death, then he manages to try and support Trip after his sister's death, openly mourns the loss of several Red Shirts in front of a Vulcan and go on to have two deep and personal talks with the man he was sure at the beginning was trying to take over his job.
The last several minutes of "Zero Hour" when everyone thinks Archer is dead.
In an odd way, Silik's death was surprisingly tear-jerking.
In "Home," Trip has to watch T'Pol go through with an Arranged Marriage. He refuses to tell T'Pol he loves her as it will only makes things worse, only for T'Pol to quickly kiss him before leaving for the marriage ceremony.
Malik's cold-blooded murder of his "siblings" Udar and Persis in the Augments arc.
The death of Admiral Forrest really came as a shock to many. It helps that he died saving Soval's life.
Trip and Hoshi dying in "Observer Effect." Even though they did get better.
The death of poor little baby Elizabeth makes the harsh comments that T'Les made about a human and Vulcan having a baby seem all the more Harsher in Hindsight.
Phlox telling Archer how Elizabeth's death hurts as much as if it was his own child.
Trip's death in the finale.
Before that, Trip and Reed's conversation in Engineering.
Tucker: Been a hell of a run, Malcolm. Never thought it would come to an end.
Reed: All good things. Captain thinks there'll be another Enterprise before too long.
Tucker: I imagine.
Reed: It won't be the same.
The real-world death of Kellie Waymire, who played recurring character and Phlox's Love Interest, Crewman Elizabeth Cutler. After her death in 2003 from an undiagnosed heart condition, the producers decided to quietly put her character on a bus and not re-cast her character out of respect.