Resources are crafting materials and miscellaneous loot. They can be found growing or laying around, and in any lootable container, including machines and humans, that Aloy finds in the world. Resources are usually highlighted in purple when Aloy looks through her Focus.
Not all items are used in crafting. Some - especially Old Ones artifacts - are only valuable to merchants for trading or selling for shards. All items (except Ridge-Wood) can be sold to merchants.
Metal Shards - Currency all items are sold for, but also used in crafting.