The friendship and romance of Arno and Élise. Especially when they were children and how Arno backs her against the Assassins despite how much it costs his standing.
Pierre Bellec's death is a Tear Jerker mixed with heartwarming when you realize that all, the time, his demeaning insult of "pisspot" to you is because of his friendship with Arno's father. He really did like Arno and it broke his heart to strike at you.
The ending of Dead Kings. Arno changes back into his original Assassin robes, having regained his optimism, and decides to remain in France. De Sade's final narration also leaves a sense of hope for both France and Arno's future.
De Sade: Ah, dear Arno. Our hopes to the future condition of the human species may be reduced to three points: The destruction of inequality between different nations, the progress of equality in one and the same nation, and, lastly, the real improvement of man.
Arno's big-brotherly friendship with Léon, and how Léon spurs Arno to have hope and take action again at the end of Dead Kings.