A Miniature History of the American Revolution blog has a set of printable flags for the Continentals.
Here’s a selection of downloadable flags for the Russian Civil War. That’s a period I’ve always wanted to paint and game. I can’t imagine a more colorful selection of armies and characters.
Here are a page of downloadable, printable flags for your American Civil War games. They’re quite nicely done.
The Warfare East site has a jpg image of Teutonic Knight banners to download, print and cut out.
The Krigsspll.dk site offers a very large selection of downloadable flags for the Crusades. They are all very well done.