MCMMO Credits can be used with /redeem to level up your skills. Each credit counts for one full level, regardless of EXP requirements.
Entropy Shards are incredibly valuable items which can be used to craft MythicDrops items of the highest tier, was well as advanced scrolls.
Repair gems can be used to repair any item to 100% durability, without disrupting it's name, enchants, etc.
Soul gems can be used for various high-level jobs crafting recipes, as well as in /soul, to teleport back to your death point.
Deus Codoxes are used to identify Unidentified Items, giving them a name, tier, etc.
Taggers add your name to an item's flavour text, as well as in its name, allowing you to personalize your loot.