I run a city based game set in Ptolus,(info from Monte's website and Banewarrens). I have one dedicated retail shop, Myreth's oddities that sells magic items. It generally sells minor to medium items, and availability of items is random,( I roll a d20 to see if an item is available).
This is not to say, that Potions, Scrolls, and some Wands are not readily available for sale from the temples in the city, as well as possibly some minor items for sale from the adventurer provisioning shops, (dungeonering in Ptolus is like the gold rush in the old west). Magic Items are also available for commision from a magical organization that monopolizes that trade.
With that said, beyond buying potions, a bag of holding, or a cloak of resistance, not much buying goes on. I also tend to differ from the normal campaign in I do not provide automatic weapon powerup/ replacements as loot. For most of my 14th level party, their magic items started out as Masterwork items, and have been enchanted by the party Druid (has Craft Arms and Armor).
Assumptions that the 3.0/3.5 rules must neccisitate Wallmart style magic items shops, are false assumptions. Historicaly, however, magic items being for sale have always been an aspect of D&D, even back in 1e days. How else were you supposed to turn all of the billions of +1 magic swords and Rings of Portection you got from any adventure Gary Gygax wrote? There is a reason why Tenser made his flying disk! In the first Gord the Rogue novel, Gary has a scene where the fine wares of a dwarvern weaponmerchant are magic items. Some degree of commerce is logical, but it does not have to be dominating.
As a DM, I think it relieves the pressure of coming up with a reason for why a particuliar item you know the player wants just happens to be in a horde, it also gives players the illusion of control, and sets up locals and NPCs the players can grow fond of, increasing the sense of reality.