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.
For people interested in original sources, the University of Michigan, the University of Oxford’s Bodleian Libraries and ProQuest have released some 25,000 texts dated from 1473 to 1700. Content is available in a variety of formats. Available immediately are some 25,000 books, with an additional 40,000 planned for the future.