For the graham cracker crust: Add the graham crackers to the bowl of a food processor and pulse until the crackers are crushed in to crumbs. Add 2 tablespoons of graham cracker crumbs to each of six 5-ounce jars. Press the crumbs down to the bottoms with the back of a spoon. Reserve the remaining graham cracker crumbs.
For the pudding: Heat the milk until hot but not boiling in a saucepan on the stove or in a heat-proof bowl in the microwave (1 minute on high). Beat the egg yolks in a medium bowl and add the hot milk, slowly at first, stirring constantly so the eggs do not scramble. Continue until all the milk is incorporated.
Add the sugar, cornstarch and salt to a medium saucepan. Whisk until there are no lumps. Slowly whisk in the hot milk mixture in a steady stream so lumps do not form. Cook over medium-low heat, stirring constantly, until the mixture starts to bubble and has thickened, about 10 minutes. Add the semisweet and unsweetened chocolate and stir until the chocolate is melted, about 2 minutes. Remove from the heat and stir in the butter and vanilla extract. Distribute the pudding among the jars and refrigerate until fully set, 2 to 3 hours.
For the toppings:
Remove the jars from the refrigerator 2 hours before serving to come to room temperature. Just before serving, top the pudding with another layer of the reserved graham cracker crumbs. Add the miniature marshmallows to cover. Use a kitchen torch to brown the marshmallows. Top each S'mores in a Jar with a large piece of graham cracker.
Propane gas torches are highly flammable and should be kept away from heat, open flame and prolonged exposure to sunlight. They should be used only in well-ventilated areas. Follow torch manufacturer's instructions for use.