The Project Auldearn 1645 blog has a nicely researched and presented set of flags for the Scottish end of the English Civil War. Just download and print.
flags
Flags For the American War of Independence
Krigsspil has a large selection of flags for the American Revolution, free for the downloadng
Making Realistic Flags For 28mm Figures
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Medieval and Renaissance Flags For Download
The Krigsspil site has a huge number of medieval and renaissance flags available for downloading.
Flags For 14th, 15th and 16th Century European Armies
Vexillia has a selection of free flags for various European armies from the 14th, 15th and 16th centuries. These include 100 Years War, Wars of the Roses, as well as Spanish, Swiss, Landsnechts, Savoyed, Venetian and Imperialist.
Look in the right hand sidebar on the page for the links.