c++ - 492 454 386
my first code golf ;)
#include<fstream>
#define B(i,j)(b[i][j]=='X')
int main(int i,char**v){for(int n=0;n<atoi(v[2]);++n){std::ifstream f(v[1]);v[1]="out.txt";char b[40][83];for(i=0;i<40;++i)f.getline(b[i],83);std::ofstream g("out.txt");g<<b[0]<<'\n';for(i=1;i<39;++i){g<<'.';for(int j=1;j<79;++j){int k=B(i-1,j)+B(i+1,j)+B(i,j-1)+B(i,j+1)+B(i-1,j-1)+B(i+1,j+1)+B(i+1,j-1)+B(i-1,j+1);(B(i,j)&&(k<2||k>3))?g<<'.':(!B(i,j)&&k==3)?g<<'X':g<<b[i][j];}g<<".\n";}g<<b[0]<<'\n';}}
A somewhat revised version, replacing some of the logic with a table lookup+a few other minor tricks:
#include<fstream>
#define B(x,y)(b[i+x][j+y]=='X')
int main(int i,char**v){for(int n=0;n<atoi(v[2]);++n){std::ifstream f(v[1]);*v="out.txt";char b[40][83], O[]="...X.....";for(i=0;i<40;++i)f>>b[i];std::ofstream g(*v);g<<b[0]<<'\n';for(i=1;i<39;++i){g<<'.';for(int j=1;j<79;++j){O[2]=b[i][j];g<<O[B(-1,0)+B(1,0)+B(0,-1)+B(0,1)+B(-1,-1)+B(1,1)+B(1,-1)+B(-1,1)];}g<<".\n";}g<<b[0]<<'\n';}}