I use them in custom Skyblock challenges.
For example a player has to collect X amount of phantom membrane.
another way that i use them is as an actual mob challenge.
The player must have at least 15 phantoms on their island at one time before they can complete the challenge. This forces players to not sleep and instead face the phantoms head on.
I know it isnt too creative, but hey a challenge is a challenge!
You could use a mob drop modifier plugin or mod to allow them to drop other items.
One of the "special" items that drop could be an item that has an OP enchant when help, but also damages the user. This would be good for offering an awesome new item, but balancing the gameplay at the same time.