J. Kenji Lopez-Alt, chief creative officer for Serious Eats, delved very, very deep into the science of making the perfect chocolate chip cookie. He's got a very specific definition of "perfect" ("...Barely crisp around the edges with a buttery, toffee-like crunch that transitions into a chewy, moist center that bends like caramel, rich with butter and big pockets of melted chocolate... with crackly, craggy tops and the complex aroma of butterscotch...that elusive perfect balance between sweet and salty").
But the food science in his piece is deep and fascinating, and provides a kind of road-map for any definition of cookie-perfection. If you've ever wondered about the chemistry of eggs, sugars, flours, rising agents and butter, and how they interact with mixing, cooking, "resting" and cooling, this is pretty much the ultimate, definitive guide thereto. I also defy you to read this without developing a craving for chocolate chip cookies.
The beauty of understanding how ingredients interact with each other is that even if my definition of the "best" chocolate cookie isn't in line with yours, if you've come along this far, then you know what you need to do to adjust my recipe to suit your own tastes. Like your cookies chewier? Substitute some of that all-purpose flour for bread flour. Want your cookies to rise up a little taller? Add a touch of baking powder or replace the yolk of one of those eggs with an extra white. You like your chocolate in distinct pockets? Just use chocolate chips instead of hand-chopped. Want your cookies more flexible and chewy? Just replace some sugar with a touch of corn syrup.