Honeycombs are used to make honey badger pouches. They can be extracted from the beehives East of Manor Farm behind the large pen. This requires insect repellent, which can be stored in the toolbelt. Extracting honeycomb is a click-intensive process as you have to right-click and select "Honey" for each one you want, though you can skip the animation of the character collecting the honeycomb by re-clicking the honey option on the same beehive.
Fill your inventory and run to the Manor Farm bank chest and back, and repeat. Use of Surge will decrease the time needed to bank. If the player has access to a Beast of Burden this can be used to further increase the amount of honeycombs that can be gathered per trip.