This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Ultraman Leo
Seven's Ultra Eye melting after he attempted to transform back in Ep.1
The death of the entire MAC force and Gen's friends. Gen and Tohru's reactions were hard to take. Silver Bloom killed hundreds, if not tens of thousands of people like every other kaiju, but this was the first time an entire anti-alien defense force was slaughtered.
An encounter between Dan and "Anne" in Ep. 29, when she repeatedly denied being her and she was playing single mom to Creepy Child Uri, whose telekinetic powers and propensity to throw tantrums put everybody (even his mom) in danger. That was Yuriko Hishimi guest starring alright, just not Anne, or so we're led to think.
The Ultra brothers' joint beam attack on Leo in Ep. 38, after Leo stood up for "Astra" Actually Alien Babalou, who had stolen the Ultra Key while the real one was in a frozen rock in space.
"Astra's" crying out for Leo to save him from being killed by the Ultra Brothers.
A few victims of collateral damage throughout, like Tohru's father and Gen's photographer friend.
Leo's dismemberment and temporary death. The writers rub salt in the viewer's wounds by having Leo say farewell to Tohru telepathicallyin the middle of the night.
Gen's frustration and anger over Alien Magma's attacks on Earth after blowing up Planet L-77.
Gen's disappearance in the first part of Episode 4. Dan himself shed a tear...
The death of Giro, which Tohru took very hard.
Yoko's death in Episode 6, which Gen was blamed for.
Episode 46 features a little girl sent by Black Star on a mission to destroy all humans. Tohro is reminded of his dead sister Kaoru. Their relationship is well shown though the only word the girl says is her name. Tears ensue.