HoneyDukes only sells chocolate frogs. When they are in your inventory you can open them to reveal the card, and add the card to your collection. You only want one of each card, so you sell multiples.the ones in the thrift shop are other people's multiples, which you can buy if you don't want to risk getting a card if you already have.
Some of the books you can read. As for ingredients, they're for a part of HOL that no longer exists, like the dueling you're supposed to be able to do with your wand. So now they're just nice to have.
The quills are what you earn for completing classes, so they're nice to have, or sell if you desperately need the beans