I tried searching the forums. There's a few that I know for sure (The great powers, I think I see Scottish/Irish flags in there, Papal States, Czech flags?).
Does anyone know who the other flags represent? I'm assuming some are just made up, but it would be cool to know for sure what flag was what. 
Let's see... from left to right, top to bottom:
Austria, Russia, Prussia, Britain, France, Spain, Ottomans, Naples, Sweden, The Netherlands, ????, Vatican, ????, Savoia, Denmark, Bavaria, Westphalia, Hannover, ????, Poland, Portugal, Italy, Brunswick, Switzerland, Cossacks(?), USA, Canada (I think), ????, Royalist France, Ireland, Finland, Japan.
Skip a few pages of random banners...
???, Ottomas, ????, ????, ????, Serbia, ????, ????, ????, ????, ????, Hungary, Austria, Bohemian nations (Croatia, Czechs, Moravia etc.), another Austrian flag(?), ????, England, Scotland, Ireland, Wallonia, ????, ????.
Hopefully this helps.