Notice that the flags below are my personal interpretation, based on hints in the books and some comments from the author on the Yahoo S.M. Stirling mailing list.
The Mackenzies’ flag is green, with silver crescent moon between antlers.
The Bearkiller flag features a stylized head of a bear, crimson on dark brown.
The Dunedain Rangers’ flag features a silver tree and seven stars.
Portland Protective Association (PPA)
The Protector’s flag is black with a “cat-pupiled” lidless eye.
The flag of Lady de Ath is descibed as “Sable, a delta or over a V argent”.
The Corvallis flag is orange and features a beaver head.
During the Protector’s War, the Mount Angel battle-flag carried the image of Virgin and Child.
The flag of Montival is described as “blue, with a green white-topped mountain, overlaid with a longsword whose guard was the crescent moon” and “the green-silver-blue flag of Montival, the crowned mountain and the Sword”.
The Bjorning tribe of Norrheim (Aroostook County, Maine) has a war-flag with a raven with a stylized “AA” on its chest.
The flag of Norland (Scandinavia/Germany) is the “Norden Flag”, yellow with a red Scandinavian cross.
The flag of Gotland is blue with a ram carrying a cross staff with a red flag.
The flag of Visby city is the same as the Gotland flag, but with red background.
Order of the Shield of St. Benedict
The Order of the Shield of St. Benedict has a flag with a cross and a raven, the Commonwealth of the Queen of Angels presumably has a different flag.