The Energy Crystal is a mid-game Industrial Craft 2 item. It's used in many of the crafting recipes for the more advanced tools and blocks, including the MFE, NanoSuit Armor, and the High Voltage equivalent of the Energy Crystal, the Lapotron Crystal. The Energy Crystal can store 100,000 EU, or the size of ten RE-Batteries.
Regardless of the tier of tool, the Energy Crystal cannot be used to recharge tools like the RE-Battery can. Similarly, without Transformer Upgrades, Low Voltage machines cannot use the Energy Crystal as a power source. The only machines that can be powered by an Energy Crystal without further upgrades are the Induction Furnace, the MFE, the MFSU, the MV Charging Bench, and the HV Charging Bench.
When used in crafting the Mining Laser, the Nano Saber, the Lapotron Crystal, and NanoSuit Armor, the charge level of the Energy Crystal determines the amount of charge the item will have. A charged Energy Crystal will produce a charged item, while an empty one will produce an item with no charge.