Shards are items used in the crafting of other items. There are six types of shards, each for the six primal aspects: Air (Aer), Fire (Ignis), Water (Aqua), Earth (Terra), Order (Ordo), and Entropy (Perditio).
There are six infused stones, one for each shard type. Each type is more commonly found in a certain biome, but they can still be found at random. However, one can expect to find Aer shards more easily in a plains biome while it would be better to search for Aqua ones in the swamp, river or ocean biomes. They roughly match the essence of each biome, so a Fire shard would be more likely to be found in a desert, for example.
Crystal clusters are created by putting together six shards, either six of the same shard for a specific crystal cluster, or one of EACH for a mixed crystal cluster. They are all weak light sources, and are great for decoration. However, if placed close to your Research Table, they provide a slow yet constant stream of research points of their respective Aspect. The Mixed Crystal Cluster gives a point to a random Aspect.