Evangelion is based on christian mythology.

While it's not fully based on mythology, there is a lot of it intertwined into Fullmetal Alchemist: Brotherhood. The meaning of Truth, the role of Sins in life, the role of Men and Women in society, the meaning of Life. A lot of it is covered in fairly abstract ways that only really reveal themselves after a few watches.

I don't think I've seen anybody mention GeGeGe no Kitarō yet, the anime/manga that single handedly revived interest in Japanese folklore and mythology.

Seven deadly sins uses a lot of biblical and mythical influences.
Trinity Blood uses the papal state as a government.
Hetalia Axis powers uses mythical representations of countries as characters, this might be a stretch.

How thin do you want to stretch it? Dragonball is based on the old Chinese myth of Journey to the West. Neon Genesis Evangelion is based on Christian myths.

Noragami is a great one about Japanese mythology.

Ancient Magus Bride has lots of Anglo mythology.

The Great Adventure of Horus, Prince of the Sun

It was originally suppose to be about the Ainu people of Japan, but that was vetoed by the executives.

Tatsuki's Kemurikusa is based on

Hozuki's Coolheadedness is all about various Japanese and Chinese legends and afterlife myths. Europe's Satan even pays a visit.

Depends on how freely you assign historical tales mythical status, but Vinland Saga contains a lot of influence lifted directly from actual Viking stories like the Greenlander Saga.

There's enough of the fantastical in both the historical sources and in the adaptation that I think it qualifies as an adaptation of folklore, if not myth.

Saint Seya, Kamisama Hajimemashita, InuYasha and Natsume Yuujinchou series came first to my mind

xXx holic has a lot of japanese myth

Inuyasha is heavily influenced by it

The Monogatari series is...adapted?

Doro he doro a bit

Natsume's book of friends has a lot about yokai and stuff, not as much mythology

The tale of princess Kaguya (one of my favorites) is a version of the old Chinese tale of the bamboo cutter

Ghost stories (English dub only - I promise) but it's any ghost stories

Heike story - I think, follows a girl who plays the biwa and can see the future, more historical

Theater of darkness - a collection of scary stories that would have their origins in myth

Kyousougiga - a story about love, reincarnation, very Japanese myth. Hard to explain but one that I loved

Thunderbolt fantasy - actually puppets, physical puppets. But more Chinese myth than japanese. It was actually a good story too

Maybe kamisama hajimemashita - a girl becomes a shrine god, a rom-com

Mushi-shi - one of my favorites, there are these spirits called musho that are more like energy and the foundation of life. They can cause issues in the world and the MC is like a physician or detective

Yuyu Hakusho was inspired by it

A lot of ghibli movies

Blood of Zeus is an obvious one

Dragonball

Using some concepts, but not really a retelling of the story:

Matantei Loki Ragnarok

Aa! Megami-sama!

Well depends on your standards. Saint Seiya is one that comes to mind, because I'm old, but as with most animes the plot has hardly anything to do with actual myth. It's just characters based lightly on mythical characters.

Fate.

the entire series is based on something else but it features a lot of mythical characters