Once you are at lvl 11 / 12 alchemist, you unlock recipes like 5% & 10% boss damage potions and such that can be crafted with hyssop flower oils.
Juniper Berry Seed oils can be used to craft wealth & exp pots, as well as resistance and invincibility potions (all of these recipes disappear within 24 hours and have a 5 min cool down between crafting each potion, however).
Juniper Flower oils (and hyssop) can be used to craft flame throwing stars, and are overall good to have to craft random potions daily, keeping your alchemist levels from degrading over time.
As for Dark Crystal, I know it is used in lvl 9 + accessory & smithing but can't think of any notable recipes off hand. I know people buy them off of me occasionally so they must be used for something