1 Make the graham cracker crumbs: Place the graham crackers in the bowl of a food processor. Process in pulses until the crackers are completely broken down into crumbs. (Alternatively: Place the crackers in a zip-top plastic bag and crush with a rolling pin.)
2 Combine the dry ingredients: Combine the graham cracker crumbs, flour, salt, and baking soda in a mixing bowl. Whisk to combine.
3 Beat the butter and sugars: With an electric mixer or in a stand mixer with a beater attachment, beat together the granulated sugar, brown sugar, and softened butter on medium speed until combined and thick, 30 to 60 seconds. Pick out any large pebbles of hard brown sugar that you see. Scrape down the sides of the bowl and the beater.
4 Mix in the eggs and vanilla: Add the two eggs and vanilla to the butter-sugar mixture and beat at medium speed until no clumps or streaks remain, 10 to 20 seconds. Scrape down the sides of the bowl and the beaters.
5 Mix in the dry ingredients: Add the graham cracker and flour mixture all at once. Beat on low speed just until no more dry streaks of flour are visible, 20 to 40 seconds.
6 Mix in the chocolate: Add all of the chocolate chips or chopped pieces, and beat on low speed for just a few seconds until incorporated.
7 Chill the dough: Scrape down the sides of the bowl and the beater. Cover the bowl and refrigerate for at least 30 minutes or up to three days. (Or freeze in individual scoops for up to 3 months.)
8 Heat the oven to 375F: Place a rack in the middle of the oven. Line two baking sheet with silicon baking mats or parchment.
I usually bake my cookies one sheet at a time to help them bake evenly. If you prefer, or are crunched for time, bake two sheets at a time with one sheet in the upper third of the oven and the other in the lower third of the oven.
9 Scoop the dough: Use a medium cookie scoop (or a well-mounded tablespoon measure) to scoop the dough out onto one of the baking sheet. Space the cookies about 2 inches apart.
10 Bake the cookies: Bake the cookies for 10 minutes, then remove from the oven. Gently press 3 to 4 mini marshmallows into the tops of each cookie. (See Recipe Note for more ways to tinker with when to add the marshmallows.)
Return the cookies to the oven and bake for another 2 to 3 minutes, until the marshmallows look like puff balls and are just starting to melt around the bottom. The marshmallows will continue to melt after the cookies come out of the oven.
11 Cool the cookies: Cool the cookies on the baking sheet for about 5 minutes, or until the puffed middles collapse down and the cookies have firmed a little. Transfer the cookies to a wire cooling rack to cool completely.
11 Continue baking cookies in batches until all the cookie dough has been used.
12 Enjoy! Cooled cookies can be stored in an airtight container with wax paper between the layers for up to a week. The marshmallows may stick to the wax paper; just gently peel the paper away when removing cookies.