Some stuff recycled from the other thread and some new:
Macross Plus - Central plot revolves around two of the main characters having a years long grudge and the pain it causes them and everyone around them. Near the end, they finally forgive each other, recognize their grudge for the petty ego contest it was, as well as one of the characters owning up to his part of the problem after being in denial about it.
Unico (Two movies: "The Fantastic Adventures of Unico" and "Unico in the Island of Magic") - Themes of love, forgiveness, friendship, self-sacrifice, living for things beyond status or ego. Plus pagan gods and magic are portrayed as evil, while main character is literally a unicorn - a symbol of Christian purity.
Cowboy Bebop - Ultimately ends in tragedy due to main character not being able to forgive and move on.
Omishi Magical Theatre: Risky Safety - Life is worth living, and you should not kill yourself, even if things go horribly wrong.
Orguss - Main character starts out as an irresponsible playboy with a Devil-may-care attitude. By the end, develops towards being a responsible adult who cares about the future and the big picture of life. Also, not to give too much away, but the consequences of his promiscuous past end up catching up with him and biting him in the butt in a major way, and play a major role in him growing into being a better person.
Kurogane Communication - Hope, friendship, and never giving up, even in the midst of the Apocalypse.
Now and Then, Here and There - Hope in the midst of horrifying suffering. Blatantly pro-life message, as woman who is raped chooses to give birth to her baby after being tempted to abort it.
Evangelion - Yes, I realize a lot of the Christian symbolism is "Ooooohh, look how cool and foreign this is!" But a lot of the symbolism is actual Kabbalistic, because ultimately the central theme is anti-Buddhism/anti-Kabbalah: saying that the ego/soul annihilation sought by these religions is a false hope, and that rather one should bear one's cross bravely throughout life in spite of the pain and suffering, because avoidance of such pain and suffering is far worse:
youtu.be/USKzAj1dOq4
Trigun - Literally created by a Catholic and subsequently has themes of maintaining a worldview of forgiveness, peace and non-violence even in the midst of a horrible and violent universe.
Macross 7: I personally hate this anime for various reasons pertaining to quality rather than moral values, but a lot of people like it, so YMMV. Main character is pacifistic and pro love and forgiveness to a fault.
Macross (original TV series and movie, and uncanonicial sequel: Macross II) - Aliens and humans war out of misunderstanding but ultimately come to peace via cultural exchange. Also themes of making peace with, getting along with and being a good Samaritan to people who may not be exactly like you.
Rozen Maiden - Learning to forgive yourself for your own sins and mess ups, overcoming the sins of despondency and despair, and having the courage to get out there and live life again.
Fatal Fury OVAs - First OVA has the main character ultimately seeking justice instead of revenge (i.e. he merely defeats his father's murderer in battle, rather than killing him in vengeance.) Second OVA has main character badly beaten and slipping into alcoholism, despondency and despair. Ultimately, overcomes his sins, with the help of caring friends, faces and defeats the adversary who beat him before. Adversary kills himself due to being overcome with the sin of pride. Main character tries to save his life, and adversary's death is treated as a tragedy. Also themes of adversary's overall mentality and death being the consequence of never coming to terms with forgiving his father.