Jolly Roger (n.)
pirate flag, attested under that name by 1724, of unknown origin; jolly here has its otherwise obsolete sense "high-hearted, gallant." Also see Roger, the sense of which here is, again, uncertain. A glossary of Banffshire words compiled by the Rev. Walter Gregor and published in 1866 gives a definition of Rodger as "anything of its kind large and ugly," also "Any animal big and ugly," also "A big person of rude manners." It also has a verb rodger "to beat with violence." Perhaps there is a connection.
Their Black-Flag, under which they had committed abundance of Pyracies, and Murders was affix'd to one Corner of the Gallows ; It had in it the Portraiture of Death, with an Hour Glass in one Hand, and a Dart in the other striking into a Heart, and Three Drops of Blood delineated as falling from it : This Flag they call'd Old Roger, and used to say, They would live and die under it. [from a description of the execution of 26 pirates in Rhode Island July 26, 1723, in Historical and Political Monthly Mercury, November 1723]
For the use of jolly, compare Jolly robin "handsome or charming man, gaily dressed man, carefree dandy" (late 14c.) also French roger-bontemps "jovial, carefree man" (15c.).