Is LEGEND part of the Pokemon name? Can I have 4 Lugia and 2 Lugia LEGEND sets in a 60 card deck?
LEGEND is part of the name, similar to past sets that contained Pokemon with "Dark" or "-ex" as part of their name. They are not considered the same as their normal counterpart, so yes you can have 4 "Lugia" and 4 "Lugia LEGEND" halves in your deck.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Do Pokemon LEGEND count as one Pokemon or two for purposes of bench space, prizes taken, attack effects, Poke-POWERs, Poke-BODYs, and calculating damage?
A Pokemon LEGEND is made up of two Pokemon cards each consisting of 1 half of the Pokemon, but it counts as a single Pokemon while in play; one bench space, one prize per KO [unless noted otherwise on the card] , etc.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Can I put three halves of one Pokemon LEGEND card and one of the other half in my deck?
Yes, that is legal if you wish. You do not need to have the same number of each half in your deck.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
How many of each half of the Pokemon LEGEND cards can I have in my 60 card deck? Is it 4 total or 4 of each half?
You can put up to 4 total halves of each Pokemon LEGEND in your deck (e.g. 4 Ho-Oh LEGEND halves and 4 Lugia LEGEND halves), but you cannot put 4 of each half of a Pokemon LEGEND in your deck (e.g. you couldn't have 4 Lugia LEGEND top half and 4 Lugia LEGEND bottom half). (GS:Heart Gold/Soul Silver FAQ; Feb 11, 2010 PUI Rules Team)
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
What if during setup the only Pokemon cards in my hand are Pokemon LEGEND halves?
Since you have no Basic Pokemon to place Active you will let your opponent look at your hand, then shuffle and redraw your hand as described in the rulebook.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Can I play a Pokemon LEGEND as my Active Pokemon or on my Bench during setup?
No. Since a Pokemon LEGEND is not a Basic Pokemon you cannot play it during setup, even if you have both halves.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Can I put 4 each of the Unown with the "RETURN" Poke-POWER and the Unown with the "FLASH" Poke-POWER in a 60 card deck?
No, you can't. In the case of cards like "Unown G" and "Unown R" where the Unown's letter is in its name, they are considered different names, and you can have 4 of each in your deck. When only "Unown" is written these are cards with the same name, so you can only put up to 4 copies of any with that exact name in a 60 card deck.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
If the Defending Pokemon is currently protected from effects of attacks, do I apply Resistance to Donphan's "Rock Hurl" attack or not?
No, because the phrase "Don't apply Resistance" is part of the damage calculation, not an effect of the attack.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Can I use Jynx's "Mimic" attack to shuffle my hand into my deck when my opponent has no cards in his or her hand?
Yes, but you won't draw any cards after you shuffle it in.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Can I use Jynx's "Mimic" attack to draw cards from my deck when I don't have any cards in my hand?
Yes, but you must shuffle your deck first before you draw.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)