Onyx Crystals are probably one of the most, if not the most valuable resource in the game. You will need thousands upon thousands of them to upgrade your equipment. There are two primary ways to get Onyx Crystals.
Some equipment that you will find throughout the game and through dungeons can be dismantled for materials. You can get to the Dismantle panel by either interacting with an Item Extractor NPC (can be seen on the minimap as a box thing) or by going to your inventory and clicking on the Dismantle option.
Players can sell their Onyx Crystals on the Black Market (some may be unable to be sold). There is one way to buy Onyx Crystals from an NPC for 2000 Mesos. To do this, you will have to not complete the Maple Guide Mission "No Such Thing as a Free Enchant." This is the third part of the crafting and enchanting maple guide so that you can complete the first two parts for the rewards. However, once you complete the "No Such Thing as a Free Enchant" mission, you will be unable to come back to the map and talk to the NPC to buy the Onyx Crystals. After leaving the map, to go back, just open up the Maple Guide and click on the big "Begin Lesson" button. This trick may not be necessary depending on the price of Onyx Crystals, but it may be a good idea to have one character that does not complete this Maple Guide Mission, so the maximum price you will ever have to pay for Onyx Crystals is 2000 Mesos. I would probably finish this mission on my main character, and leave it up on an alt because you will always see the quest available to you, which may be annoying.
For equipment that you cannot dismantle or sell on the black market, feel free to store it in your bank if it’s not character bound to give to another character that can use it, or sell it to an NPC for some money. If you can't sell it or dismantle it and you don't need it anymore, just throw it away.