I'm married to an EU citizen and I have my EU marriage certificate apostilled. I'm currently in my native country, but I want to visit Europe. Can I apply for the visa for every Schengen member country or I can only apply the visa for the country of my spouse?
You should apply to the country you are going to, like every other visitor. If you happen to go to the country your spouse is from, different rules might apply but otherwise the visa should be free of charge.
These rules only apply if you are travelling with your EU spouse (or to join him or her). If you are travelling alone, then you have to apply for a Schengen visa following the regular procedure, with all the supporting documentation and associated fee.
See also Travel documents for non-EU family members on Europa.eu.