Prepare the dough: Measure 1 1/2 cups warm water in a liquid measuring cup or bowl. Whisk in the yeast until completely dissolved. Allow to sit for 5 minutes.
In the bowl of a stand mixer fitted with a dough hook attachment (see notes for other mixing/kneading methods), beat the flour, brown sugar, and salt for a few seconds on medium speed. With the mixer running on medium speed, slowly drizzle in the yeast mixture making sure to scrape out yeast with a spatula.
Switch mixer to low speed and mix until all the flour has been worked into the dough. The dough will look shredded; that's ok. Once it appears this way, increase the speed to medium and knead for 8 minutes. The dough is incredibly stiff and will be somewhat dry; do not be tempted to add more liquid. During the 8 minutes, if the dough splits or breaks apart-- stop the mixer and fold the dough back together with your hands-- then continue to knead until smooth and cohesive.
Lightly grease a large bowl with oil or spray with nonstick spray. Shape dough into a ball and place in the bowl, turning it to coat all sides in the oil. Loosely cover the bowl with aluminum foil or a clean kitchen towel and allow the dough to rise at room temperature for about 90 minutes. You want the dough to be larger and puffy, but not quite doubled in size.
Line two large baking sheets with parchment paper or silicone baking mats. Place a wire rack over a third baking sheet. Set all three aside.
Shape the bagels: When the dough is ready, gently punch it down if you notice any air bubbles. Turn it out onto a clean surface. It will still be a little stiff-- not sticky. Divide the dough into 8 equal pieces. Just eyeball it. Makes no difference if one is slightly larger than another. Shape each piece into a ball and place 4 balls onto each of the two lined baking sheet. Then, hold up one ball and press your index finger through the center to make a hole. Poke two fingers through and widen the hole by rotating your fingers in a circular motion. You want the hole about 1 1/2 - 2 inches in diameter. Repeat with remaining dough balls. Cover the shaped bagels with a damp kitchen towel and allow to rest as you prep the water bath.
Preheat oven to 425°F (218°C).
Water bath: Fill a large, wide pan with 2 quarts of water. Whisk in the honey. Bring water to a boil, then reduce heat to medium or medium-high so that the water remains simmering. Drop bagels in, 2-4 at a time, making sure they have enough room to float around. Cook the bagels for 1 minute on each side. Transfer each bagel to the wire rack with a slotted spoon. They will look a little shriveled-- that's ok!
Topping: Mix together the poppy seeds, sesame seeds, dried minced onion, dried garlic flakes, and coarse salt in a bowl. Using a pastry brush, brush the egg wash on top and around the sides of each bagel, then sprinkle each with the 'everything topping' mixture; OR you can dip the top of each bagel directly into the 'everything topping' mixture.
Place 4 of the bagels back onto each of the lined baking sheets. Bake for 20-25 minutes, rotating the pan halfway through. You want the bagels to be a dark golden brown. Remove from the oven and allow bagels to cool on the baking sheets for 20 minutes, then transfer to a wire rack to cool completely.
Slice, toast, top, whatever you want! Enjoy your homemade everything bagels.
Make ahead tip: These bagels freeze wonderfully! Freeze them for up to 3 months, thaw overnight in the refrigerator, then warm to your liking.