Since I'm working on my Burgundians I'm using this to keep a record of my references and links.
Top site - Simon Chick's Je Lay Emprins, lovely 28mm figures.
A useful summary of the ordonnance companies flags (mainly low resolution copies from the Freezywater book (link)
Tom Oberhofer's Charles The Bold page has details of coinage and the battles of Grandson, Morat and Nancy (link)
The Muerten (Morat) Panorama has nice details (link)
Freezywater (Lance & Longbow) - The Burgundian Army of Charles the Bold
Hobilar (L&L Journal) Issue 19
Osprey - Armies of Medieval Burgundy, 1364-1477
WRG - Armies of the Middle Ages, Volume 1: The Hundred Years' War, the War of the Roses and the Burgundian Wars, 1300-1487
Casterman(Funcken) - Armies de touts les Temps - one of the medieval pages covers Burgundians
Richard Vaughan's books on the dukes of Burgundy - take your pick on whichever ducal reign you're covering - still best history published in English.
Wargames Soldiers Strategy 64 - the battles and sieges of Charles the Bold. Issue 30 covered the Burgundian-Swiss wars.
Renaissance Armies by George Gush, contains a chapter
Valois Burgundy by Vaughan, which compliments the 4 ducal titles
Artillery of the Dukes of Burgundy by R D Smith and K Devries
Plenty of excellent images on Dansk Figurspilsforenings
Some useful ones on Warflag
Lance & Longbow - Freezeywater flags using the same artwork as the book above.
Pavises - some decals from Little Big Men (28mm though)
Donnington Miniatures has a couple of Burgundian flag sheets
I'll be adding more as I find it, but any other useful references/links please let me know.
Thanks to Simon and Bob for the updates so far