You can get small-value Rupees by cutting grass, killing mobs and breaking pots. Bosses each drop a Silver Rupee when killed. Some even have a chance to drop multiple Silver Rupees. Use Rupees to buy things from villagers or upgrade your equipment.
Potions & Chu Jelly
There are 3 different colours of Chu Jelly that can be made into Potions of the same colour.
Blue Jelly comes from Slimes that are killed using the Four Sword and its potions restore Hunger.
Red Jelly comes from Slimes that are killed using the True Four Sword and its potions restore Health.
Green Jelly comes from Slimes that are killed using the Master Sword and its potions restore both Hunger and Health.
Simply craft an Empty Bottle from glass and fill it with Jelly. You can also fill it with Milk from a bucket. Unlike Milk Buckets, these can stack.