Break 1 package of the unsweetened chocolate bar into pieces. Add the chocolate and butter to a microwave-safe bowl and heat in the microwave for 1 minute. Stir well, then microwave for an additional 60 seconds until the butter is completely melted. Stir until smooth.
Combine the sugar and the melted butter and chocolate mixture in a large mixing bowl. Add in the eggs and vanilla. Add the flour and mix well. Refrigerate the dough for 1 hour until firm.
Preheat the oven to 350 degrees. Shape dough into 1-inch balls and place at least 1 inch apart on ungreased baking sheets. Bake the cookies for 6-7 minutes at 350 degrees, just until set. The sides should be set but the top still shiny. Use a spatula to transfer the cookies to a cooling rack and cool the cookies completely to room temperature.
Chocolate ganache: chop 1 package semi-sweet baker's chocolate bar into small chunks; place the chocolate in a small mixing bowl and set aside. In a small saucepan, heat the heavy whipping cream over medium heat just until it begins to simmer. Pour the hot cream over the chopped semi-sweet chocolate and let it stand for 5 minutes. Whisk the chocolate and cream together until well-blended then let stand for 15 minutes to thicken. Spoon the chocolate ganache over cookies.