I have 5 games that use controlers -- Anomaly: Warzone, Guilty Gear X2, Defence Grid: Awakening, Devil May Cry 4, and Fahrenheit. Of these five, 2 were purchased from GOG.com (GGX2 and F), two from Gamer's Gate (DMC4 and A:W), and one from Steam (DG:A). Of these, only the two from GOG.com fail to work properly. In the case of GGX2 its a simply case of "can't map the right buttons to the right function". In the case of F, buttons (as well as the right stick) aren't being mapped at all.

I have a Logitech controler F310 which has a switch to go between two standards -- the Xbox standard, and whatever was used before that. I tried both. No luck. In the case of GGX2 the button mapping is different, but still wrong. In the case of F it only registers when set to XBox controls.