Meanwhile, melt the butter in a medium saucepan over medium low heat. Whisk in the flour, and cook for about 5 minutes, stirring constantly to avoid sticking and burning.
Once the flour is cooked, stir the wine into the flour mixture slowly. Use a whisk to smooth the mixture. Slowly add cubes of Gruyere, Cheddar, and Emmentaler cheese; stir until cheese is melted. Transfer cheese mixture to fondue pot. Keep warm over low flame.