No; all you need specify is 'Weapon Focus: Ray,' and the feat will apply to all rays.The 3.5 PHB states that you can take the 'Weapon Focus' feat for Rays.
Does that mean you have to specify 'Ray of Frost' or 'Scorching Ray'
when you take it (for example)?
Yes. In the Complete Arcane there is a feat called Ranged Spell Specialization that requires Weapon Focus: Ranged Spells and caster level 4th, which might be a better feat for ya. Though there are no improved versions, so if your DM is a stickler for RAW, it might not.What about Weapon Specialization? Can that feat apply to Rays as well?
No; all you need specify is 'Weapon Focus: Ray,' and the feat will apply to all rays.
Yes. In the Complete Arcane there is a feat called Ranged Spell Specialization that requires Weapon Focus: Ranged Spells and caster level 4th, which might be a better feat for ya. Though there are no improved versions, so if your DM is a stickler for RAW, it might not.