Duke introducing the Joes to his parents as his "new family." Manly Tears.
Not part of the show's canon, but the dedication to character designer Clement Sauve, the show's character designer who passed away earlier this year, at the end of "Brothers of Light" is this for the show's entire production crew.
After the Joes win yet again in "Castle Destro," the Baroness expresses concern over Cobra Commander's reaction. Destro states he will take full responsibility for the failure to protect her.
Also the ending for the Joes, where the team assures Duke that they would follow him anywhere.
The relationship between Tunnel Rat and his brother Teddy Lee. The two are completely dedicated to eachother.
Crossing into Tear Jerker territory, the flashback with the death of the Hard Master. He took a sip of tea while Snake Eyes was about to do the same and, as he realized he had been poisoned, the Master still had the lucidity to knock the cup out of Snake Eyes's hands to avoid him the same destiny. It later turns out Snake Eyes's cup had no poison in it, but it doesn't make that last act of affection of the old man for the boy who changed him for the better less poignant.