If a Gloom Confused you, and next turn a Magmar Smokescreened you, do you flip for Confusion or Smokescreen first?
Checking for Confusion should be the very first thing you deal with after announcing what attack you want to use. So as soon as you announce your attack, the check for Confusion happens immediately. If that passes, then you flip for Smokescreen's effect.
Source: WotC Chat (2000-07-13), TPCi Rules Team (2014-09-25), TPCi Rules Team (2016-01-07)
My Koffing used its "Smokescreen" attack on the Defending Pokemon which was already Confused. If that Pokemon attacks during my opponent's next turn, do they flip 2 coins and the attack fails if both coins aren't heads?
No, your opponent must flip each coin separately. First, flip a coin for the effect of Confusion. If the first flip is heads, then flip a second time for the effect of Smokescreen.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11), PUI Rules Team (2014-09-25), TPCi Rules Team (2016-01-07)
If your Pokémon has been Smokescreened on the previous turn, and you choose an attack that requires you to do something (such as discarding Energy) in order to use the Attack, do you pay the attack costs before you flip for the Smokescreen Effect?
Yes before, you still attempt the attack; the Smokescreen might just stop it from having any effect.
Source: WotC Chat (2000-04-13), WotC Chat (2001-04-05)
What about cards that do not state when the effect ends? Like Fossil Magmar's Smokescreen? I think for only one turn (the opponent's next turn), but some Apprentice people say it lasts until Magmar is Benched!
The effect says tries to attack during your opponent's next turn, so it only works on the next turn after you use the attack.
Source: WotC Chat (2000-05-04)
When Smokescreen stops an attack, does it stop all effects of the attack, even those that might be done to the attacking Pokémon?
Yes, it stops all effects.
Source: WotC Chat (2000-05-04)
If you use Smokescreen then retreat the Pokémon that is Smoke screened or if Magmar Retreats is it still in effect?
Smokescreen references the defending Pokémon, so if you bench that Pokémon the effect ends. If you bench Magmar then Smokescreen is in effect.
Source: WotC Chat (2000-04-06)
If Magmar's Smokescreen Knocks Out the Defending Pokémon, does the new Active have to flip to see if its attack is effective?
No, it only effects the Defending Pokémon the attack was done against.
Source: WotC Chat (2000-02-24)
Does Magmar's Smokescreen effect end if the Defending Pokémon evolves?
Since Magmar's Smokescreen attack references the Defending Pokémon, by it evolving, it removes that effect.
Source: WotC Chat (2000-02-03)