Skill Focus and Skills with Specializations

A skill with different Specializations (such as Knowledge or Perform) is still only one skill. Thus, if you take Skill Focus in one of these skills, you get the +3 with all Specializations areas you possess now, or gain in the future.

Skill Focus and Craft/Profession

Craft and Profession are broken into separate skills, not specializations (you have to pay 1 skill point per rank in each type of Craft or Profession, rather than getting your full number of ranks for 1 skill point).

This means that if you take Skill Focus in Craft, you have to specify which type of Craft it is, and gain no bonus on other forms of Craft. The same applies for Profession.