Position oven rack in center of oven, and preheat to 400°F Spray the inside of the muffin tins and the rims with nonstick spray or put the paper cups inches If you are using silicone, spray as directed then place them on a cookie sheet.
Place the chocolate and butter in the top of a double boiler set over simmering water. If you don't a double boiler, use a heat safe bowl the fits snugly over a small pan of simmering water. Stir constantly until the chocolate and butter are half melted. Remove double boiler/bowl from heat then continue stirring, away from the heat until smooth. Cool for 10 minutes.
Meanwhile, whisk the flour, baking soda and salt in a medium bowl until well blended. Set aside.
Once the chocolate mixture has cooled, whisk in the eggs one at a time, making sure the first is completely incorporated before adding the second. Whisk in the sugar until completely dissolved. Then whisk in the milk and vanilla until smoot, about 2 minutes.
Stir in the prepared flour mixture with a wooden spoon until well blended. Do not overmix.
Fill the prepared muffin pans 3/4 full. Save leftover batter for second batch. Bake for 20 minutes or until the muffins have pale brown, smooth, rounded tops and a toothpick comes out clean.
Set the pan on a wire rack to cool for 10 minutes. Gently rock each muffin from side to side to release. Remove from pan and set on rack to cool for an additional 5 minutes more then serve. If storing or freezing, let cool completely before storing in airtight containers or freezer bags. These muffins will stay fresh up to 24 hours at room temperature, or up to 1 month in the freezer.