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.
Clan Mackenzie
The Mackenzies’ flag is green, with silver crescent moon between antlers.
Bearkillers
The Bearkiller flag features a stylized head of a bear, crimson on dark brown.
Portland Protective Association (PPA)
The Protector’s flag is black with a “cat-pupiled” lidless eye.
Mount Angel
During the Protector’s War, the Mount Angel battle-flag carried the image of Virgin and Child.
Montival
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 Bjornings
The Bjorning tribe of Norrheim (Aroostook County, Maine) has a war-flag with a raven with a stylized “AA” on its chest.
Norland
The flag of Norland (Scandinavia/Germany) is the “Norden Flag”, yellow with a red Scandinavian cross.
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.