In general stores:
When a player wants any of the common goods (soap, a candle, a bedroll), the general store basically has it. Sometimes I will throw in story elements "A bedroll? I have a few moth-eaten blankets, but if you go down the road to Ms. Murphy, she makes wonderful bedrolls". Of course, Ms. Murphy has a side-quest the players can spend an hour or 2 on for a break from the main quest.
In specialty shops:
In a true niche store, either there will not be much stock, or there will be bogus stock. In a magic store in a low-medium magical setting (like in Shadowrun, there's enough magic for stores, but it's not ubiquitous like it is in some games/settings) there are likely useless fetishes, charms, and similar things for the gullible to buy and think work, but the proprietor likely knows all the magic-users in town and has a box of the "good stuff" whenever those magical folks come in looking for a new magical item/accessory.
In a more "general" specialty shop, they will have what makes sense, and refer any other business to either another specialty shop, or the general store down the street. The stable will sell horses, mules (and other beasts of burden), their tack and saddles, but pretty much nothing else. The Smithy will stock horseshoes (because he makes them), and weapons, but won't likely sell/fix saddles... that's the something the livery should be able to sell/fix.