The way Christianity is being portrayed in anime is in the same level as that of portraying French or English culture. It is primarily added to bring about a certain look and feel, but also because the story/plot has some relation to the religion mentioned.
Shinto is frequently a theme in Japanese popular culture, including film, manga, anime, and video games. Shinto religion is at the core of Japanese culture and history and as such greatly affects the outcome of pop culture in modern Japan.
In the Beginning: The Bible Stories (手塚治虫の旧約聖書物語, Tezuka Osamu no Kyūyaku Seisho Monogatari, lit. Osamu Tezuka's Old Testament Stories) is an anime television series based on The Bible's Hebrew Scriptures (Old Testament) created by Osamu Tezuka.
Gokuism seems to be a newly emerging religion that is based on the moral example of the protagonist in the Dragon Ball series: Son Goku. It is not an officially recognised religion, but rather a shared creation of fans on the internet.
Masashi Kishimoto is a Buddhist manga writer and through his work of Naruto was able to incorporate Buddhist values and characteristics to the manga/anime. Buddhism is what helped form the creation of Naruto.
My Last Day is a 2011 Christian anime short film created by The Jesus Film Project, with Barry Cook and STUDIO4°C. The story unfolds through the eyes of a criminal who receives the same crucifixion sentence as Jesus Christ.
First light novel volume cover featuring the title character, Violet Evergarden. A 13-episode anime television series adaptation by Kyoto Animation aired between January and April 2018 with several advance screenings taking place in 2017. The series was awarded Best Animation at the 2019 Crunchyroll Anime Awards.
The Animated Bible Series, currently in production, is the world's first visual narrative of the entire Bible from creation and the fall to the kings and prophets, to the coming of the Christ and His final Revelation.