I know you can throw chocolate bars down the wishing well and enchant an item. Are there any other uses for them or should I just throw them all down there?
You can create Pain au Chocolat to get a bonus of 15% to magic, power or health
Be careful with how you use your chocolate bars as there are only 13 in the entire game.
If you want to know what enchantments you can make, here is the full list. This list is taken from the candy box 2 wiki.
Throwing one into the wishing well will permit you to enchant the:
Leather Gloves to pink enchanted gloves or red enchanted gloves. Octopus King's Crown to Obsidian or Jaspers versions. Monkey Wizard Staff to an enhanced version that spits stronger spells more often. Tribal Spear to an enhanced version that summons tribe warriors that will fight by your side. Knight's Body Armor to reduce the damage taken by 80% but divides damage dealt by the equipped weapon in half. Giant Spoon to an enhanced version that does 315 damage and has an incredibly slow weapon speed.