Here's one method.
Hmmm... here's a thought: The socketed item begins life with an enhancement bonus equal to the number of sockets plus one (or two or three or whatever). It acts like an item with that enhancement bonus until something is placed in one of the slots, then it loses a point of the enhancement bonus and gains the appropriate socketed ability. So a three-socket +1 longsword would count as a +4 weapon with nothing in the sockets or a +1 flaming burst orcbane longsword with two rubies and an orc's fingerbone in its sockets.
Mechanics-wise, this method doesn't alter the price of the item because the cost of the item is based on the number of sockets (also duplicating rarity from Diablo 2). The cost of the additional flexibility is offset by the fact that only socketable items have to be of a certain value (gems must be worth, say, 500gp or more?) and, once placed in a socket, can not be removed without a lengthy, expensive and difficult to get magical ritual.
It does open up a new level of munchkinism, but it would suit a hack-and-slash focused campaign.