Valvatorez' "pep talk" to Desco at the end of Chapter 3. Desco's just been beaten and the veneer of last-boss-ness she was putting on has been stripped away completely, leaving behind the truth of a sad little girl who was abandoned by the person she loved, and now she's afraid she'll never measure up or be welcomed by anyone. Val's reassurance to her that she can be a final boss and his promise to her to make her into a magnificent final boss is the perfect mix of heartwarming and bizarre that you only find in Disgaea.
The normal ending when Valvatorez tells Nemo, who believed he was beyond forgiveness, to become a Prinny and earn his forgiveness rather than giving up his soul. Because he is the Prinny Instructor, Valvatorez says he will personally ensure that he will work to pay off his sins. Finally, there's Valvatorez's last line which ends up being used in a more uplifting and heartwarming way compared to its usual application:
Also from the ending, everyone encouraging Emizel to reap his first soul.
Emizel: In the name of Death Emizel, I hereby sunder thy soul from this life.
Fuka realizing that despite feeling that she had been neglected, her dad truly loved her. That he didn't become a mad scientist out of remorse for his late wife but to fulfill the wishes of her daughter and created Desco and Des X because Fuka really wanted a sister. ...then she hits him for making her really strange sisters.
The growing sisterly bond between Fuka and Desco, especially during the Fuka and Desco Show. Of particular note, Fuka telling Torn Desco that regardless of how unshakable the rules of reincarnation are, she will not let it take away her memories of her precious baby sister and all her friends.
The Vulcanus aka Artina ending. She talks with Val, and after the usual Snark-to-Snark Combat, finds that Val still won't drink her blood because of his promise. Her response? He can, because she was so scared of losing him to the malice.
The Netherbattle Tournament finally throwing Prism Red a bone by having Nisa become his first legitimate friend. That squeal of delight he lets out can easily bring Tears of Joy to even the coldest of hearts.
ANY of the character-specific epilogues count, as it really hits home just how great a leader and mentor Valvatorez is to his party.