Tsumiki no Ie - 12 minute movie without any dialogue. Won an Oscar as Best animated short film in 2009 (and deservedly so) but is still often overlooked. ~#950 in MAL popularity.
Satoshi Kon movies like Perfect Blue and Millennium Actress - Way more well-known than Tsumiki no Ie, but still nothing I ever see people talking about despite being great movies.
Aku no Hana - Stop judging a show entirely on your first impression of the art style, seriously...
Bartender - Not quite as good as the aforementioned titles, but still a series I consider quite underrated (ranked below #1000 on MAL).
Satoshi Kon movies like Perfect Blue and Millennium Actress - Way more well-known than Tsumiki no Ie, but still nothing I ever see people talking about despite being great movies.
Aku no Hana - Stop judging a show entirely on your first impression of the art style, seriously...
Bartender - Not quite as good as the aforementioned titles, but still a series I consider quite underrated (ranked below #1000 on MAL).