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Tear Jerker: Indiana Jones and the Kingdom of the Crystal Skull
Indy looking at a photo of the late Henry, Sr., complete with the musical cue from the previous film.
Early on in the movie, Indy reveals that Marcus and his father both died, and with Mac betraying him, he's completely alone. This brought tears, only for a reprise of crying when Indy finds Marion and Mutt again.
The line by Indy's friend Charles (Jim Broadbent): We seem to have reached the age where life stops giving us things and starts taking them away.
Thankfully that later lead to a happy subversion (as well as a happy tear-jearker) when Indy got Marion back, found out he had a son, and both he and Charles get their jobs back.
Not to mention the way John William's score is precisely aimed to work these moments to the hilt. I now can't hear the Grail theme without tearing up at the thought of Henry Jones Sr's death.
Mutt's angry reaction when he finds out Indy is his father. Thankfully he warms up to the idea after awhile.
Irina Spalko's fate is slightly sad in that despite what she kept saying about using the skulls power to help the USSR rule the world. Her true hearts desire was nothing more than wanting answers to the questions man has asked since our humble beginnings. Unlike Belloq's greed, Mola Ram delusions and Donovan's obsession with obtaining eternal youth. Spalko's desire seems almost innocent by comparison.
Innocent, perhaps, but not very bright. Maybe the expression "there are some things man was not meant to know" is the best way to put it.
Especially given that the novelization reveals that the aliens even forcefed her knowledge of ancient eldritch beings. Also, she very much felt her dematerialization.