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If I remember correctly, the PC boxes in Gen IV are able to hold all 493 Pokemon, 1 from each species. If my PC was totally full, I'd just release any extra Pokemon in the PC that I have.
If that were to happen, I'd probably buy another copy of the game. After all, it would have taken me a lifetime to complete my Pokedex, and I woudn't just throw all my work out the window for breeding, haha.
If that happens, (which is impossible, because majority of my PC spots are for useless Pokemon) I'd probably release some and minimize catching some Pokemon.
Completing the Pokedex was never my game, so I wouldn't think of this... for now.