The Chain Spell feat can be applied to any spell that normally has a single target. However, it is unclear what happens in cases where spells (such as stoneskin) have expensive material components, or in cases where spells (such as wish) have experience point costs. Do these material/experience costs need to be paid per target of the chained spell, or are they paid just once (for the initial target) and the secondary targets of spells chained this way are "free"?
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You use your materials once: mainly simply because it doesn't specify otherwise.
Chain Spell involves casting your spell once on one target, and then the effect arcs from target to target. There's no reason it should require casting your spell multiple times, or sacrificing the resources equivalent to doing so.
You're only casting the spell once, so the cost is not affected.
Now, neither stoneskin nor wish actually meet the criteria for Chain Spell. To apply the feat, the spell must:
Stoneskin has a range of touch, and spells like wish or miracle don't specify a single target. (You can use them on a single target, but that's true of all multi-target spells!)
There are some tricks that could extend the range of stoneskin, but at that point you're investing substantial resources into a trick that's not that OP to begin with. There is probably some combination of spells and other abilities involving the feat that is somehow broken, but that's true of a lot of things in 3.5.
RAW, they are free. Chain Spell is specific about what happens, and expensive/XP components are required to cast a spell, not to affect a target. Absent any special rule in Chain Spell (of which there is none), they do not get duplicated.
Whether or not this is a problem is hard to say. You don't obviate the cost entirely; hitting more targets usually won’t be too big a problem, not at three spell levels. Bring metamagic reducers into it, and use spells already very powerful despite the cost, though, and you have problems...