Is Zakah (obligatory charity) due on articles of merchandise even if they were stacked in the merchant`s stores for years?

Yes, Zakah is due on goods even if they were stacked in merchant`s stores for years, in this manner Islam struggle against monopoly.

Is it permissible for the doctor to uncover the hair of a female patient out of necessity?

It is only permissible for him to do so when there is no female doctor, and he should examine the patient in the presence of one of her Mahrams (unmarriageable kin).

What is the ruling on working for a company that manufactures cigarettes?

All Perfect Praise is due to Allah, The Lord of The Worlds

Working for a company that manufactures cigarettes is forbidden because smoking itself is forbidden, so its production, selling and circulation are forbidden as a result since they aid in committing sin, and whoever aids in that is like the sinner himself. And Allah Knows Best.

What is the ruling on having brotherly ties between a strange man and a strange woman, and is the former considered a Mahram (unmarriageable) to the latter?

Such a relation between a strange man and a strange woman is forbidden in Islam because it involves forbidding what Allah has allowed by marriage, and allowing what Allah has forbidden such as looking and the like. Such a relation doesn`t render any act lawful between them, thus they are forbidden to look at each other, have a Khulwah (seclusion), and travel together.