This is a hard one for me ... but rather than try and objectively define what makes something a masterpiece in an all-comprehensive way I will mention that one quality that helps for a series to qualify for this is re-watchablility.
And a few I can name off hand would have to be Kemono no Soujo Erin; the Clannad series is also amazing for me; and the Aria series, definitely the Aria series.
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