If you have a metamagic feat that raises the spell level slot required, then the cost of the item increases accordingly. For example, a scroll of Burning Hands would normally cost 1*1*25gp to create, but if it were done with the Enlarge Spell feat (which requires using a spell slot one level higher and doubles the range) then it would be a 2nd level spell, which requires a minimum caster level of 3, so the cost would be 2*3*25gp, or 6 times higher than the other version.
If you have a feat that doesn't actually increase the level at all (like Eschew Components from the Forgotten Realms) then I suppose the cost wouldn't be increased, or you could house-rule some sort of extra cost (maybe 10%)? Then again, the 0-level increase feats mostly wouldn't apply (you don't really worry about Eschew Components when making or using a scroll anyway...).