Energy Damage is a broad term used to describe most non-physical attacks. Fire and Cold are the most common forms of naturally occurring sources, while a acidic pool or lightning strike would be examples of Electrical or Acid damage. There are many types of less natural types as well.
All damage listed in the Wiki is BASE damage. It is then modified by whatever element it takes on. For Example Fire Storm inflicts 1d6 fire damage per CL, which is modified up to 1d8 per CL
Acid damage wears and tears at creature more then simply damage. All Acid damage has it's damage dice reduced by one step. A d6 would become a d4. In addition whenever a creature or object suffers Acid damage it has all resistences reduced by 1 for every 5 points of damage dealt. The reduction lasts for 1 minutes and is refreshed whenever any amount of Acid damage is taken.
Electric damage is increased by 50% if the target is flying, falling or otherwise more then 5ft above the ground. When ever a creature takes Electrical damage they take -1 on initiative for one round per 5 points of damage taken. The penalty refreshes and is cumulative if additional Electrical damage is taken prior to the penalty expiring.
Fire damage is most effective against flammable objects and creatures. The searing flames increase the base damage dice by one step. A d6 would become a d8 against most creatures and objects unless one is especially non-flammable, such as a wall made of stone would only take standard d6's. Most creatures outside of constructs take this additional damage.
Cold damage is creeping and insidious. The damage dice of Cold damage is reduced by one step. A d6 would become a d4. In addition, whenever a creature takes cold damage it becomes hindered for 1 round. If cold damage is applied to wounds it must make a Fort save equal to the damage dealt or become Immobilized on a successful save they are instead Hindered. If a creature was already Hindered and take Cold damage to woulds it is automatically Immobilized for 1 round. If an object takes Cold damage it has it's hardness reduced by 1 for every 5 damage dealt, regardless of whether or not the damage is resisted by hardness. Flexible objects become rigid and brittle. A object moving or rolling on the ground imediately ceases movement and is frozen in place. (This does not work on a falling or flung object. It must be incontact with another solid surface.)
Sonic damage is extremely effective against most objects. Any rigid or crystaline object takes double damage from Sonic damage and hardness is ignored unless the object is magical. Crystaline or sound sensitive creature may take an additional 50% damage and have the damage dice increased by two steps.
Anarchic damage is made of distilled chaos. Anarchic damage deals double damage against object but cannot deal damage to an object with the broken condition. In addition before damage is rolled flip a coin. If heads all damage is increased by 50%; if tails all damage is reduced by 50%.
Holy damage is pure righteousness. When inflicting Holy damage you may have it harmlessly cascade against and living creatures unless they are Evil Outsiders, Undead, Aberrations, or is an Evil Dragon.
Primal damage is incarnate nature and the energy that came before. Primal damage can ignore some natural life. When inflicting Primal damage you may have it cause no harm to Animals or Plants. Primal damage crashes harmlessly off natural structures and unhewn stone. Against artificial structures the damage is doubled but does not ignore hardness. This has no affect on objects that are not apart of a structure. A magically shaped tree or stone is immune unless it was changed to appear artificial.
Unholy damage is hate, lothing and evil manifest. Unholy damage allows the user to have it dissapate without dealing damage to Undead, Evil Outsiders and Evil Dragons.