Special Conditions can stop your Pokémon from attacking or using Poké-Powers, and give your opponent time to build up their board. Some decks, like Flariados, even make it a central part of their strategy. Here are some ways of dealing with them:
Special Conditions are removed upon moving to the Bench.
Retreating also works, but Paralyzed and Asleep Pokémon cannot retreat.
This removes Special Conditions (and a damage counter) from non-ex Pokémon.
It can wake Jirachi up after it puts itself to sleep with Wishing Star and simultaneously provide the Energy for its retreat.
With a basic Grass Energy attached, it provides Special Condition immunity for the attached non-ex Pokémon.
One advantage it has over Heal Energy is that it can remove existing Special Conditions if attached via Electrode ex's Extra Energy Bomb.
A Holon Mentor-/Dual Ball-able answer to Special Conditions.
Vaporeon ☆ has a similar Power.
Provides partial Special Condition immunity for Darkness Pokémon.
Note that it does not stop Poison or Burn (which is intentional, as there is a Cacturne that can inflict Poison with its Poké-Power if Sidney's Stadium is in play).
Grants a Heal Energy effect to any Energy, but only for Water/Fighting/Metal Pokémon.
Since Jirachi is a Metal Pokémon, Island Cave works like Heal Energy for it.
With a basic Water Energy attached, it prevents effects of attacks (which includes Special Conditions) done to the attached non-ex Pokémon.
Note that it does not stop Special Conditions from Poké-Powers/Bodies, such as from Espeon ☆ or Flareon ex.
Green Essence is a Holon Energy GL-like effect, but less restrictive (works with rainbow Energy, and on ex's).
Played in some Dragonite ex δ builds.
Evolving, like switching out, removes Special Conditions. Sometimes it pays to go slower and save Evolutions in hand to defend against Special Conditions:
Suppose you have a Nidorina with 2 Energy on it, ready to evolve into the Nidoqueen in your hand, but your opponent has Stantler. The bad play would be to evolve into Nidoqueen immediately and use Toxic — your opponent can counter with Screechy Voice, leaving you stuck with a Confused Nidoqueen and an underdeveloped Bench. Instead, you should save the Nidoqueen and use Fast Evolution, building up your Bench next turn with the Evolutions you pulled. If your opponent uses Screechy Voice, you can then evolve to Nidoqueen (removing Confusion) and attack back with Toxic, or even Power Lariat for the KO.
Suppose you have a Shuppet with 1 Energy on it, and your opponent has Stantler. If you mindlessly use Ascension, they can Screechy Voice and Confuse your Banette (ex). What you should do is pass; build up your Bench instead while waiting on Professor Elm's Training Method or Banette. If you topdeck either of those, you'll be able to evolve into Banette, attach an Energy, and use Night Murmurs, which will leave them with a Confused Stantler.