Does a breath weapon's area of effect always have to extend to its fullest size, or could you use it over a smaller area than your maximum if you so chose (e.g. breath weapon is 60 foot line, stop line at a particular target instead)? If this is possible, does it require a feat or any other prerequisite?
In a stricter reading of the RAW, I think the answer is yes, a breath weapon's area of effect always extends to its fullest size / covers the maximum area possible, and causes the damage given in the rules.
(and the DMG3.5 has the very same information.)
Considering that - as far as I know/remember - even to split its breath into two equal portions (or to change the shape of the breath) a dragon (the most obvious example of a breath weapon user) has to have a feat (a separate feat for my two examples), I don't think it likely that it would be possible to limit a breath weapon's area and/or damage without a feat. (Think of it as if the creature had a gun. When the creature fires the gun, the gun projectile travels a distance and causes a damage that only a specialist, highly trained gun-wielder can try and control.)
Of course, there might very well be a book or an article that modifies the above, but I haven't encountered any (but other answers are quite likely to bring them up, if there's any.)