Taken from lists by Shinchosha Magazine, Laputa Animation Festival, Tokyo Anime Award Festival, Cut Magazine, Animage Magazine, Kinema Junpo, and the Japan Media Arts Festival.

Original Lists:

Laputa Animation Festival:
www.nishikata-eiga.com/2010/10/laputas-top-150-japanese-and-world.html
www.nishikata-eiga.com/2011/02/30-treasures-of-world-animation.html

Shinchosha:
www.reddit.com/r/anime/comments/6z2spq/top_anime_and_anime_directors_voted_by_japanese/

Tokyo Anime Award:
otakuusamagazine.com/anime-festival-ranks-top-100-anime-of-last-100-years/

Animage:
popgeeks.com/forums/threads/animage-top-100-anime.63067/page-9

Japan Media Arts Festival:
web.archive.org/web/20110824141758/http://plaza.bunka.go.jp/hundred/list_anime.html

Cut Magazine:
patrickmacias.blogs.com/er/2006/11/mama_inai.html

Kinema Junpo:
www.nishikata-eiga.com/2010/10/kinema-junpo-top-10-animated-films-2010.html
letterboxd.com/oscarkit316/list/kinema-junpo-best-1970s-japanese-film-poll/
letterboxd.com/eiganerd/list/kinema-junpo-1980-japanese-film-best-15/
letterboxd.com/eiganerd/list/kinema-junpos-best-ten-japanese-films-of/
mubi.com/lists/best-japanese-movies-of-the-2000s-kinejun-readers