There are a variety of ways to get percentage discounts on crafting costs. Before delving deeply into specifics, it's worth discussing how they stack. The D&D rules for stacking apply explicitly to modifiers (with a separate section on spells which is much less clear and thankfully not applicable here).
Since these are percentages, they require multiplication, and here is what the SRD has to say on multiplication:
Sometimes a rule makes you multiply a number or a die roll. As long as you’re applying a single multiplier, multiply the number normally. When two or more multipliers apply to any abstract value (such as a modifier or a die roll), however, combine them into a single multiple, with each extra multiple adding 1 less than its value to the first multiple. Thus, a double (×2) and a double (×2) applied to the same number results in a triple (×3, because 2 + 1 = 3).
When applying multipliers to real-world values (such as weight or distance), normal rules of math apply instead. A creature whose size doubles (thus multiplying its weight by 8) and then is turned to stone (which would multiply its weight by a factor of roughly 3) now weighs about 24 times normal, not 10 times normal. Similarly, a blinded creature attempting to negotiate difficult terrain would count each square as 4 squares (doubling the cost twice, for a total multiplier of ×4), rather than as 3 squares (adding 100% twice).
There are separate rules for abstract values and real world values. Money, and by extension price, is a real world value, but the platonic base price of a magic item is certainly abstracted from the real world price; it doesn't factor in the added costs of material components or XP, or whatever discounts on purchasing a buyer might have. XP, unlike money, is fairly clearly an abstract value, not a real world one. Here in the core rules, it's unclear if we multiply or add cost reducers (in fact, there's a reasonable argument to be made that, RAW, we multiply cost reducers for gold and add them for XP, which is horrible). Luckily, we have more evidence for how to interpret the rules.
We can refer to the Unbound Scroll, a class from Dragonmarked, who gains an ability called Master Scribe (Ex):
When you use Scribe Scroll, reduce the gp and XP costs by 5% for each level in this class. These bonuses stack with those of Legendary Artisan and Extraordinary Artisan, so that a 5th-level unbound scroll with the Legendary Artisan feat reduces the XP cost of scroll creation by 50%.
The authors of Dragonmarked, at least, certainly thought that crafting cost reducers stacked additively, and defined stacking as additive in RAW. Unless one wants to make the assertion that Master Scribe stacks additively but other reducers stack multiplicatively, which seems extremely tenuous, I would say that crafting cost reducers do, in fact, stack additively. That's also more in line with D&D math, which simplifies wherever possible.
And so, with that in mind, it's not all that difficult to reach a 100% discount on crafting.
- Craft Wondrous Item
- Magical Artisan (Player's Guide to Faerun): This feat allows its user to, "When determining your cost in XP and raw materials for creating items with this feat, multiply the base price by 75%." It's best to parse this as a 25% cost reduction. Magical Artisan can technically be taken multiple times, but since it refers to the base price it won't stack with itself, and will need to be applied before any other cost reducers.
- Bind Elemental (Eberron Campaign Setting): CL 9, requires Craft Wondrous Item, costs reduced by 20% as per the rules in Magic of Eberron (requires a colossal elemental to stuff into the item).
- Legendary Artisan & Extraordinary Artisan (Eberron Campaign Setting): Costs reduced by 25%.
- Extract Demonic Essence (Fiendish Codex I): XP costs reduced by 50%. The item may become cursed, but it's probably fine.
There are a variety of 10% cost reducers one could accrue to discount the final 30% gold cost: various affiliations from the Dungeon Master's Guide II, the artificers' dump location from Dragon 350, the Apprentice (craftsman) feat from DMG II, and so forth.
A word of warning: in the SRD, there are options to reduce the value of magic items by 10% if they require a specific skill, or by 30% if they require a specific class or alignment. As KRyan points out, these affect the actual market value of the item rather than its base cost, and thus are applied in a different step than normal crafting cost reducers (and consequently end up being multiplicative). Additionally, since they affect market price, their affect on crafting price is only half of what it seems, since a crafter pays half the market price in gold (with some exceptions).
Now, obviously crafting magic items without cost isn't particularly appropriate for most campaigns, but crafting is an inherently broken system, arguably the most broken system in 3.5. The artificer is trivially more powerful than a wizard in medium to highly optimized games (outside of combat, an artificer casts spells from scrolls as a every spellcaster in the game, but 2 levels higher—it's absurd). Even a non-optimized group can realize the problems when the druid decides to carve a club for shillelagh and realizes that, because a club is free, crafting it is instantaneous.
So, while it may seem absurd that one doesn't have to resort to abusing wish or other spells to get 100% free magic items, it's par for the course for crafting in 3.5.