One trick I am fond of is to introduce treasures which are, effectively, material components for the creation of magic items which may have a cash value of X but when applied to a particular item (or type of item) it is worth some multiple of X (5X is a decent rule of thumb, but some may be more or less). What form these items take is a function of your campaign setting—they might be monster gizzards, elemental gems, relics of an ancient race, or whatever—but the bottom line is that they're specialized to make a narrower band of items and (implicitly) the feat is required to identify and process them.
Thus, the "cost" of making a magic item is the same as if you buy it under normal conditions because residuum is fungible. It is equally viable for any type of magic item, and is the main stock in trade, especially because it's predictable and stable. Merchants are far less likely to carry specialized components because a) there's less guarantee of resale, and b) fire gems tend to explode when shaken and brined beholder eyeballs have a bad habit of moving on their own.
Net result: by adventuring after the appropriate components, players can drastically reduce the cost to construct a particular item.
Now, this has some flaws. First, you need to decide how to value the components when it comes to treasure parcels. Whether they count as their sale value, their specialty value, or something in between depends a lot on how strictly you adhere to the rules for cash and treasure parcels. I'm assuming that if you want to do something like this it's because you want to have players be able to get magic items without being as wealthy as kings, so that should not be a problem—just continue to play it by ear.
Second, you need an arrangement with your players that they not just use these components to make items, then disenchant them into residuum. That would be cheesy and undercut the whole point. If you need to start tracking "disenchant value", then do so. It actually adds an interesting twist to these things if component cost doesn't come back when disenchanting, so the payoff of disenchanting any given item may actually be lower than expected, introducing a bird-in-the-hand kind of idea.
Alternately, if the hang up is the smell test, just make the currency of the dominant power a residuum (rather than gold) standard. It's a little hokey, but it makes things seem a little less silly, and you just add a small "processing fee" to enchantment and disenchantment (so, like currency exchanges, they're technically equal, but the guy making the exchange always gets a cut).