Which boot*.s file I should choose?
Generally speaking,
boot0 looks to load boot1 from the first active HFS partition.
boot0hfs looks to load boot1 from the first bootable HFS partition.
boot0md looks to load boot1 from everywhere
(A proper description can be found
here).
Boot0md has pretty much superseded boot0hfs and you would use either boot0hfs or boot0md when dual booting with Windows from a different partition on the same HDD as OS X.