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)
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)
Can I use cards that search for a Pokemon, like "Bebe's Search" or "Poke Ball" to get a Pokemon LEGEND card from my deck?
Any effect that lets you search your deck or discard pile or do something from your hand with "a Pokemon" will let you use that effect on one half of a Pokemon LEGEND set, but not both halves.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)
Can I use "Pokemon Collector" to choose Pokemon LEGEND cards as part of the 3 Basic Pokemon I search for in my deck?
No, because Pokemon Collector only lets you choose Basic Pokemon. Pokemon LEGEND are considered "Unevolved Pokemon" when in play, but they are not considered "Basic Pokemon".
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)