I'm assuming you've cloned whatever you want to keep already?
What Shaymin do you have? I think the one I have is Oblivia. I'm curious which Rayquaza you have as well as there was a nice Event one out with V-create learned (cannot be learned except via Events, and so far Rayquaza and Victini each have one). Also wondering about Deoxys; again, I have an Oblivia one. I have two Jirachi now, and Celebi is considerable because mine's been used in the Castelia City bit (making it useless for trades as it can't be used).
Action Replay. Cloning code. Basically I take the original (in the box), hold R, and move it to a blank spot in the box (not swapping with another Poké, effectively "killing" it and with the same end result of cloning), releasing R after finishing the move.
You don't see it at first, but if you leave the box and return, you find the second (or third, or fourth, or...) Jirachi (or Arceus, or Darkrai, or...) in your box where the original was, or in the case of multiples, at every PC location that it touched. You can put it in one empty PC box and quickly clone 29 more to go with it. I'm doing this with Emerald imports into SoulSilver; I have one staying in SS, and one in Unova. Usually the clones move to Unova. I'll breed these with Ditto eventually to make stronger versions of them for my breeding shop (open someday); since my Ditto is flawless, it should sooner or later create the perfect specimen of any species if I inbreed.