I like to keep my deck and discard pile sideways to help me keep them separate from my bench. Is that OK?
Your deck must be oriented vertically, to avoid revealing information during handling or cuts. You may turn your discard pile 'sideways', to help you distinguish it from your bench.
Source: PUI Rules Team (2008-10-16)
Can you have 4 Electivire and 4 Electivire Lv.X in the same deck?
No, Lv.X Pokemon are considered the same as other pokemon with the same name. You may only have a maximum of 4 combined in your deck (i.e. 3 Electivire, 1 Electivire Lv.X).
Source: PUI Rules Team (2008-09-25)
Can I have 4 Deoxys Attack Forme and 4 Deoxys Speed Forme in my deck?
Yes, the "Forme" is part of the name, so you can have 4 of each.
Source: PUI Rules Team (2008-08-07)
Is it required to have a Basic Pokémon in your deck? For example, could I make a deck with just the fossils and no other Basic Pokémon in it?
Starting with EX:Delta Species, there is now a requirement to have at least 1 Basic Pokémon in a deck in order to be considered a legal deck.
Source: PUI Rules Team (2006-01-12)
Can a World Championship deck card be used as a local language reference?
Yes, it can be used. The card is not being played in a deck, it is being used as a reference.
Source: PUI Rules Team (2005-02-03)
Can you mix Team Magma and Team Aqua cards in the same deck?
Yes. There is no rule preventing you from playing rival teams in the same deck. The cards generally work better within the same team, but it's up to the player how they build their decks.
Source: Team Magma vs Team Aqua FAQ (2004-03-04)
Can you have 4 Electabuzz and 4 Electabuzz-EX in the same deck?
Yes, you can play 4 Electabuzz and 4 Electabuzz EX in the same deck, as they are considered different cards (similar to the ruling for Trainer Pokémon).
Source: PUI Rules Team (2003-09-11)
Can you have more than 4 Metal [Special] energy cards in a deck legally?
No. [Ed. Note: Same rule applies to Darkness [Special] Energy too.]
Source: WotC Chat (2000-12-21)
Can I have say 4 Blaine's Arcanine and four regular Arcanine?
In one deck? Sure, they have different names.
Source: WotC Chat (2000-06-22)
Can I have an English Dark Blastoise on the side while having a Water Energy with Dark Blastoise written on it in my deck and play it in a tournament?
No, you'll have to use the Dark Blastoise.
Source: WotC Chat (2000-05-04)