The crystal is a glowing blue shard that Penn comes across while trapped in the Nothingness in "Save the Worlds". When Phyllis notices that he has it in his back jean pocket, she takes it and reveals that it is a key to finding Penn's parents, Brock and Vonnie.
The crystal is the first major lead in the search for Penn's parents so far.
The second crystal is discovered by Maria (inside the Treasure Chest) at the end of the first episode of Season 2, it's unknown if Penn will travel back to the Pirate World to get it (as he didn't know it was inside the chest in the first place).
When Penn's MUHU tracks down the third crystal in the beast world, it distract him from the mission, even when he obtain the third crystal, he still needs the second crystal from Maria.