From Creatures Wikia
Honey is a delectable treat in Creatures 1 that is savoured by Norns and Grendels alike! When a world is first created, six honey pots are scattered in random locations. Each honey pot may be eaten from several times before it is emptied. Upon emptying a honey pot, it may be refilled by a Norn or the Hand by simply dropping it in front of the beehives above the learning computer.
Honey is also present in Creatures 2, where the pots are bigger. They still get emptied eventually, though, and must be put under a beehive to be refilled.
Sadly, the Shee do not appear to have been fond enough of honey to take any with them when they left Albia, and there is none in the Docking Station or Creatures 3, despite having 3 beehives in the Norn Terrarium.
There are many COBs and agents that create or use honey: