In Kanto (requires 8 badges and beaten Pokemon champ once for access), in Pewter city there is a museum. go in and on the far right there is a scientist that will take all your fossils and turn them into Pokemon.
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You can only get the Helix Fossil in Pokemon HeartGold. This means that to get an Omanyte or Omastar in SoulSilver, you must either trade for one or trade for a Pokemon holding one.
old amber, dome fossil and maybe some more
to get fossil Pokemon in heart gold and soul silver in pewter city someone in pewter museum says he revives fossils and you can get them using rock smash in ruins of aiph and other places.
Must trade Cranidos appears in Diamond/Platinum (odd ID number) - Revive Skull Fossil
no you can trade soulsilver pokemon to black