At the end of a long match, I Selfdestruct Magneton. My opponent and I both take our last Prize cards. Who wins?
Well, if one of you has a Benched Pokémon to replace your Active Pokémon and the other player doesn't, then the person who can replace his or her Active Pokémon wins. Otherwise, you play Sudden Death. This is explained in the Pokémon rules in the Expert Rules section under "What Happens if Both Players Win at the Same Time?"
Source: WotC Chat (1999-10-04)