Fruits and vegetables can be eaten as is and depending on quality you will get stronger moodlets. They can be replanted, they can be sold, they can be used in cooking to reduce cooking costs. Curtain mods make it so cooking REQUIRES you to have certain fruits or vegetables in inventory to cook. You know, INGEDIENTS. Plasma Fruit can be used as a full grown (No pun intended) food source for vampires, making your garden into farm.
Fish can be sold for money, can be used as decoration, can be kept in fish bowls, one specific fish is needed to make Ambrosia.
Both Fish and fruits/vegetables can be used as a fertilizer, with fish in general being better one.
SO yeah. A LOT of uses.