This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Flint the Time Detective
Artie, whose bond with a young Auguste Rodin is incredibly close, clings, sobbing, to Auguste when the time comes for Flint and co. to take him away forever. The boy promises to never forget him...before having his memories forcefully wiped clean. For the remainder of that episode, Artie never stops crying. Honestly, it's like seeing Pikachu taken away from Ash with a little Mind Rape thrown in for good measure.
In fact, whenever Time Shifters befriend various figures throughout history, it's a given that they'll get no happy ending.