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In the DS Yugioh games you could set one card in the deck to get some special effects whenever it is used in a duel as the signature or boss card of the deck. That was a really nice touch. I guess you could use those Pokeball effect things but that's DPP only.
I'd like to say mine is Porygon-Z, but I tend to use Lanturn more than Porygon-Z in battles.