Brown the butter: In a light-colored saucepan, melt butter over medium heat. Continue cooking, swirling occasionally, until butter turns golden brown and smells nutty (about 5-7 minutes). Pour into a heat-safe bowl and refrigerate until solidified but still soft (about 1 hour or overnight).
Preheat oven to 350°F (175°C). Line two baking sheets with parchment paper.
In a medium bowl, whisk together flour, baking soda, and salt.
In a large bowl, cream together the softened brown butter, granulated sugar, and brown sugar until light and fluffy (about 3 minutes with an electric mixer).
Beat in applesauce, vanilla extract, and honey until well combined.
Add peanut butter and mix until smooth and creamy.
Gradually stir in the dry ingredients until just combined. Don't overmix.
Drop rounded tablespoons of dough onto prepared baking sheets, spacing cookies 2 inches apart.
Create the classic crisscross pattern by pressing each cookie with the tines of a fork dipped in sugar.
10 If desired, sprinkle cookies lightly with flaky sea salt.
Bake for 10-12 minutes, rotating pans halfway through, until edges are lightly golden and tops have slight cracks.
Let cookies cool on baking sheets for 10 minutes before transferring to a wire rack to cool completely.