Can you "Energy Trans" or "Dark Trance" a Rainbow Energy, Multi Energy, or any other special energy cards?
As long as they are providing the proper energy type and don't violate any other restrictions written on the card, then yes you may.
Source: PUI Rules Team (2004-05-06), PUI Rules Team (2005-11-17)
If I have Quagsire and my opponent has Ampharos-EX in play and I attach an energy card to my Quagsire from my hand, which Poke-POWER gets applied first, Saturation or Conductivity?
Conductivity and Saturation happen at the same time, so the player attaching energy would get to decide which effect to apply first.
Source: PUI Rules Team (2005-03-03)
Would Flygon's "Energy Shower" attack set off Ampharos-EX's "Conductivity" power? Like if I set down 6 energy, it would do 60 Damage (however I set down the energy)? And if yes, would the damage be done to Flygon or to each separate Pokemon. that I attach an energy to?
Yes, Flygon would indeed trigger Ampharos-EX's Conductivity; it also works the same way for Azumarill's "Drizzle" attack. And the damage would be done to each individual Pokemon that gets an energy attached to it.
Source: PUI Rules Team (2004-01-29)
If Porygon2 has changed a Grass energy to Lightning, would it be fair to say that Venusaur could not Energy Trans it (for the rest of the turn)?
Correct.
Source: WotC Chat (2002-01-17)
If I have 2 of the same Pokémon in play that have a Pokémon Power [or Ability], can I use that power twice? What powers wouldn't be useable twice, or more for that matter?
Sure, depends on the particular power though. If you had two Muks for example, then only one power is necessary.
Source: WotC Chat (2000-05-11)