if i want to play shapshifter, and i took some fighter class, since pretty much every form uses unarmed attack, so doesn't it help if i weapon specialize in unarmed attack?

Guess it could help, but most people who use the unarmed route like to take monk for the wisdom ac bonus, feats, spiffy saving throws and unarmed attack bonus.

I assume you arent talking about actually taking the shifter prestige class, as loads of the shapes you get from that use weapons. If you are and still want to multi with fighter for weapon specialisation, then battle axe, spear, longsword and short sword are good choices.

Is far as I know, unarmed damage and damage from natural weapons do not stack.

Weapon Focus: Unarmed does NOT help a Shifter. Improved Critical: Unarmed DOES, however. Makes no sense, but there you have it. Weapon Focus feats DO work for the Shifter shapes that use weapons.