Good beer cheese fondue recipes are available on SamuelAdams.com and EatWisconsinCheese.com. The Samuel Adams' recipe is made with saison beer, whereas Wisconsin Cheese's recipe is made with amber beer.
To make Samuel Adams' fondue, combine 12 ounces of saison beer with 1 chopped garlic clove in a fondue pot, and boil over high heat. Reduce the heat to low and simmer for 10 to 12 minutes. Increase the heat to medium and stir in 1 pound of grated Gruyère cheese, 1 pound of grated Comté cheese and 2 pounds of cheddar cheese.
Cook until the mixture is smooth and add 1/2 teaspoon of powdered mustard, 1/8 teaspoon of cayenne, and salt and pepper to taste. Mix in 1 teaspoon of honey. Stir 1 tablespoon of cornstarch into 3 ounces of saison beer and pour into the fondue. Whisk until smooth and serve with cubed bread and apple wedges.
To make Wisconsin Cheese's fondue, melt 3 tablespoons of butter over medium heat and stir in 2 tablespoons of flour. Slowly whisk in 1 cup of milk until smooth and add 2/3 cup of amber beer. Gradually whisk in 1 1/2 cups of smoked and shredded gouda cheese and 1 1/2 cups of shredded cheddar cheese.
Once smooth, whisk in 1 teaspoon of Dijon mustard, 1/2 teaspoon of Worcestershire sauce and 1/4 teaspoon of cayenne. Season with salt and pepper to taste. Serve with Italian breadsticks and slices of baguette.