Well, Crown of Glory: Emperor's Edition is a bloody good game about the French Revolutionary and Napoleonic Wars (Started an AAR of it in the General Games forum a while ago, never got around to finishing the 2nd turn though
).
They have a bunch of AGEOD's old games (Wars in America, Napoleon's Campaigns, American Civil War), but they are published by Paradox now AFAIK. I have only the newer Rise of Prussia (Which was published after Paradox bought them, so not Matrix Games), but I heard they were quite good.
Then you obviously have the other games in the Airborne Assault series, Highway to the Reich and Conquest of the Aegean, which are very good.
They have a few other games that look intersting, but I haven't had a chance to play them yet.