Where can I find them? There are a few outside Mardaneus' house in the beginning of the game, but since honey is so useful, I'm looking to get more pots to carry with me. Empty flasks won't work. :(

Honey temporarily raises Str/Agil/Int by 5, then restores 50 MP and HP. There are only so many honey racks and empty jars in the game, and once they’re gone, that’s it.

You will find everything you need to gather honey at Mardaneus's house early in the game. It is scarce after that and rarely found. I used it in the first catacombs. You will find a few jars later in the game but not often enough to make it useful on a regular basis.