There are two different things here - your essence, and your village's essence. Your essence is the bar, which you use to cast spells. The village's essence is the number next to the lightning bolt, which your towers and such use.
For your essence, there are several ways to replenish it:
(1) Let time pass. It slowly increases over time.
(2) Dead bodies give off small amounts of essence, as do trees and other plants when you chop them down or harvest them. If you wave your hand around areas with those things, you'll get some essence.
(3) If you hold your hand over an essence collector (which has essence), essence will be drained from the collector to you.
(4) If you use the Grab spell to drop something (creature, resource, item, whatever) into a cullis gate, it will give off essence, which you can collect with your hand. Be careful not to drop too much too quickly, as a gate can overload, causing it to be damaged. Like any other building, if it gets too damaged, it will be destroyed. However, unlike most other buildings, you cannot repair ancient cullis gates (i.e. the ones that start the game on the map). You can, however, repair cullis gates that you yourself have built.
(5) The Dissolve spell can be used on trees, crystals, and whatnot in order to dissolve them, giving off essence, which you can then gather with your hand. Cast it in the right spot (e.g. a forest, so as to dissolve a bunch of trees), and you will get back more essence than it cost to cast the spell in the first place.
For the village's essence:
(1) All of the things above (except for "Let time pass") work, as long as you have essence collectors (which are not already full). Just don't wave your hand around the loose essence, and the essence collectors will attract it. So for example you can dissolve some trees and then move your hand away; your essence collectors will then get the essence.
(2) Additionally, essence collectors can "eat" crylithium, which creates essence. It's not an immediate thing - it creates essence over a period of time. I think the created essence gets put into the air, and then sucked back to the collector, so if a collector eats some crylithium, and then fills up on only a small amount of the essence that the crylithium created, I think that the "extra" essence can then be sucked up by other essence collectors (or your hand).
(3) When lightning rods are hit with lightning, essence will be created, which can then be sucked up by collectors or your hand.
As for the crystals -> essence life cycle:
(1) A crystal harvester harvests a crystal.
(2) The crystal is brought to a crystallery, either directly by a crystal harvester, or later by a crystaller or an organizer.
(3) A crystaller converts the crystal into crylithium.
(4) The crylithium is brought by a crystaller or an organizer to an essence collector.
(5) The essence collector eats the crylithium and generates essence.
Crystals grow back naturally over time, and crystal "forests" can expand, just like regular tree forests. An appropriately placed crystal motivator will increase the speed.
One little trick to keep in mind: The Motivate Land spell can be used to regrow stuff that you have dissolved. So you can use forests and whatnot as a sort of battery system, storing up essence during the bountiful times and harvesting it during the lean times: When you have enough essence and nothing really is going on, Motivate Land on some forest or whatever outside of your town. When you need essence, Dissolve that forest. With respect to this, note that Motivate Land works much better when it's raining (no matter whether naturally or via the Storm spell).
I... think that's all I know about essence?