In Ali Soufan's book The Black Banners, he explains the title by noting that quotes from various Hadiths regarding "Black Banners" of a "new army" taking over Khorasan have some kind of prophetic significance with many modern adherents of extremist jihadism.
He notes that it is "not a coincidence" that Osama bin Laden made al-Qaeda's flag black.
Soufan also notes that there is debate about whether the prophet Mohammed actually spoke some of the quoted Hadiths (such as one attributed to Abu Hurairah).
In some forms of racing, a black flag is used to disqualify competitors or indicate some other penalty (such as a forced pit stop in NASCAR).
In The Lord of the Rings set several thousand years subsequently, the good Dúnedain bore a flag with solid black background as their royal standard, charged in silver with depictions of heirlooms from the founding of Gondor and Arnor including the Palantiri and the White Tree.