The stores in the game: Sherman Exports, Jackson Store, Deep Core Mining, Hartman Group, Stockman Store, Baskin Exports, and Vanzant Traders sell a subset of the different resources in the game.
The stock level of the stores is increased by people selling that same resource to Joes or TKD in-game, and is decreased by people buying the resource from any location or branch of the store. The stock of the store is not increased automatically by the game at any point.
For example, if Sherman Exports is currently out of Hyper O2, Hunbaba shoots a ship, loots 8 Hyper O2, and then sells the 8 Hyper O2 to Joes at Starbase-51, Sherman Exports on Krall II will then show a stock level of 8 Hyper O2.
Then if Hunbaba then buys those 8 Hyper O2 back (at close to four-times the price) from the Sherman Exports on Jerico, which then shows Hunbaba that Hyper O2 is sold out, the stock level of Sherman Exports on Krall II will then also be sold out.
Do keep in mind there are over 1,000 players in the game, so the stocks of these stores can fluctuate quickly at times.
UPDATE: Jan 2010
Due to massive fines imposed on Commercial Services, all players resources that would normally be lost when a player is removed from the game (for any reason) will now be sent to a storage facility used to help fund and stock the 7 'Fair Trade' companies. These NPC driven companies will find resources delivered to them at irregular periods of time.
The use of the 'Fair Trade' agreement will mean that rather than valuable resources being lost when players or settlements are removed they are returned to the community.