Third party mods can make new capacitors that Ender IO will use just like the built-in ones. There are two ways of doing so: Programmatic and NBT. The programmatic way allows you more control but gives you a compile-time dependency on Ender IO. The NBT way doesn't do either.
Implement crazypants.enderio.base.capacitor.ICapacitorDataItem on your item. It only has one method, getCapacitorData(). This will be called to retrieve the data object (ICapacitorData) from an ItemStack when it is inserted into a machine. The capacitor data will then be queried every time a value is needed (one notable exception is the machine's energy buffer size, which is only set once).
ICapacitorData also is a quite simple interface, virtually everything happens in float getUnscaledValue(@Nonnull ICapacitorKey key). The single parameter is a ICapacitorKey, one of the pre-defined keys in Ender IO that represent all the different values Ender IO's machines have. There's a CapacitorKey for the energy buffer size of the Sagmill, one for the stack size limit of the Farming Station, one for cost of copying a coordinate paper in the Dialing Device, etc.
getUnscaledValue() then needs to produce a capacitor level for the CapacitorKey. This is not the final value, but the quality of the capacitor for this specific use. The 3 'normal' capacitors have the levels 1, 2 and 3 for all uses. The level getUnscaledValue() produces should stay between 0 and 5. Values outside this range could produce serious malfunctions.
NBT-base capacitors work the same way as programmatic ones, just that there is no getCapacitorData() on the item. Instead the ICapacitorData is created from the NBT tags of the ItemStack. This means that the NBT data has to contain a complete mapping of all possible CapacitorKeys to a capacitor level. To achieve that, the NBT data can contain level data in 4 different ways: LEVEL, TYPE, OWNER+TYPE, NAME. When looking up a value, Ender IO will try to find a value in reverse order.
Note: The examples on this page are incomplete NBT snippets and need to be combined according to what's written in the descriptions. TL;DR: Copy&Paste without reading won't work.
{eiocap:{level:1.111f}}
A LEVEL definition is required for all capacitors to be valid. This is the ultimate fallback value.
If an item that has durability has a NBT capacitor applied to it, then it will damage the item for 1 point each time the machine it is in completes a task.
{eiocap:{amount:2.222f}}
{eiocap:{area:2.222f}}
{eiocap:{energy_buffer:2.222f}}
{eiocap:{energy_gen:2.222f}}
{eiocap:{energy_intake:2.222f}}
{eiocap:{energy_loss:2.222f}}
{eiocap:{energy_use:2.222f}}
{eiocap:{speed:2.222f}}
Every CapacitorKey has a TYPE. The type is a rough categorization of the purpose of the key.
{eiocap:{"enderio:block_simple_alloy_smelter":{energy_buffer:2.222f}}}
{eiocap:{"enderio:block_simple_alloy_smelter":{energy_intake:2.222f}}}
{eiocap:{"enderio:block_simple_alloy_smelter":{energy_use:2.222f}}}
...
In addition to a TYPE, capacitor keys are also specific to a machine.
{eiocap:{"enderio:block_simple_alloy_smelter/intake":2.222f}}
{eiocap:{"enderio:block_simple_alloy_smelter/buffer":2.222f}}
...
And the most specific way is to target a specific CapacitorKey by its name.
Note: This list only contains some samples that may even be outdated. Please look up the availables names in the xml recipe files (e.g. capacitor.xml, capacitor_machines.xml).