Tear Jerker / Gankutsuou

• Near the end of Episode 12, Albert gets thrown out by Danglars and his guards, and is distraught as he makes his way to the exit; when he sees the Count, he seems to be in shock. The Count, realizing his presence, asks him what's wrong as he approaches him. Albert's emotions burst through and he breaks down as he runs into the Count's arms. The Count can only hold him as he cries, and looks genuinely concerned for him.
• Near the end of Episode 15, the Count sends Albert back to Earth, but not before holding his hand and bidding him farewell. When he turns away, Albert is left confused and hurt at the realization that he may never see the man he looks up to and admires again. Albert runs to him to try and catch up to him while calling out to him, but no matter how hard he runs, the Count is getting farther and farther away. All this time, the Count's face is hidden in shadows, and his head is slightly tilted downwards, and when he and Albert both stop, there is a glimpse of the Count's face as he tries not to look at the friend he's betrayed. When Albert begs him not to send him away, the Count can no longer maintain his stiffened posture, and his mask slips as he turns to look at him. The look on his face is no less than heartbreaking. As he gazes at Albert one last time before the trust between them is destroyed, you can almost see him being torn apart on the inside, because he really wants Albert to stay, and it's killing him because the betrayal of their friendship is one of the prices he has to pay to carry out his revenge. As the doors close and Albert cries out to him to let him stay, we get a close up shot of his eyes, and the Count just looks so... HEARTBROKEN. Once Albert is gone, the Count reaches out his arm, as if trying to grab hold of Albert, before he breaks down and mourns the friendship he's betrayed. You can practically hear his heart breaking as he cries... And then Gankutsuou takes over....
• Though it's inevitable given his painful naïveté, watching Albert break down repeatedly and blame himself as disaster and betrayal rain down on him towards the end of the series, all because his good friend the Count is losing his humanity to the desire for revenge.
• The death of Franz.
• The Count's duel with Franz as a whole, really. Hearing the poor fellow scream in agony, and Mercedes sobbing and begging, while the Count just won't stop. Even worse if you know that it's actually Franz in there. Even worse still if you know that he's not going to make it.
• When the Count tells Albert about his past, when he was Edmond Dantes and betrayed by his friend and associates, the episode flashes back to Edmond being shipped off to the Chateau D'if, begging to know what he's been accused of and screaming that he's innocent. In the prison itself he's used as a biological component of the fortress' defence system, and over the years he's driven to madness and attempts at suicide, bashing his head against the walls of his cell and swearing revenge on those who took everything from him...which attracts the attention of Gankutsuou...
• Haydee finding the Count in a pained and weakened state before his confrontation with Fernand. She begs him to take his medicine, which he refuses to do, and when she tearfully makes her Anguished Declaration of Love, he gently holds her hand and kisses her on the forehead before telling her that her words no longer reach him because his only desire is to see his revenge through. Despite the way he treated Haydee after she demolished Fernand Mondego's presidential campaign, that kiss was his way of saying goodbye and trying to console her before Gankutsuou takes over. Especially with what happens after...
• The begging, nay grovelling done by Fernand to Edmond in order to save the life of Albert. What's especially moving is that Fernand himself shot his own Albert in rage a short while previously due to the heat of the moment, when Albert tried to stop Fernand from killing Mercedes when she decided to finally leave him for good, and now here he is, abandoning virtually all of his dignity just to save his own son's life from his one-time childhood best friend and now mortal arch-enemy.
• The Count - no - Edmond's death. Haydee is holding his hand, and he squeezes it in response as he takes his final breath.
• In the final episode, one can't help but feel that if Edmond had survived, he might have found peace with Haydee and his other servants in Janina.
• The response of Mercedes when she visits the graves of both Edmond and Ferdnand in the final episode.
• As a matter of fact, Edmond's past and the last two episodes, especially when Haydee attempts to stop the Count, when Albert hugs him, and when he dies.
• The glowy flashback scene showing Edmond, Mercedes, and Fernand during their younger years, with Mercedes' hat flying off and the two of them going after it. Just the whole way that Mercedes acted like a cute Tsundere, and the playful and innocent way that they got along made for a rather depressing contrast to what you know happened later.
• The opening. The shot of Franz, Eugenie, and Albert walking by the sea becomes especially painful near the end of the anime, since it references both the memory Franz recalls as he dies and a similar scene from Edmond, Mercedes, and Fernand's youth (mentioned above).