Crystals are mysterious items found throughout the game world.
The crystals have a use, but are not a main story point yet, But according to the Devoloper, Dasius, they will eventually be a main focal point for the game's story. 
The Four CrystalsEdit
There are Five known crystals as of the 0.0.9e update. They are the Dark Crystal (Fear), Light Crystal (Protection), the red/orange crystal [fire], and the blue crystal [water], And the Green Crystal [Earth].
The Crystal's use. Edit
Contained inaccuracies and spoilers, Section was changed.
They have a use, and it isn't just "being lights" Searching for the answer is part of the fun.
Side-Note - If your crystals are flubbernucked, Slipcor's v0.0.9e save-fixer has a feature to reset them.
<ref>tags exist, but no
<references/>tag was found