Mathematica - 179 163 154 151 chars

    a = {2, 2, 2};
    s = Export["out.txt", 
       CellularAutomaton[{224, {2, {a, {2, 1, 2}, a}}, {1,1}}, 
                (ReadList[#1, Byte, RecordLists → 2>1] - 46)/ 42, #2]〚#2〛
       /. {0 → ".", 1 → "X"}, "Table"] &

Invoke with

    s["c:\life.txt", 100]

Animation:

You can also get a graph of the mean population over time:

A nice pattern for generating gliders from Wikipedia

AFAIK Mathematica uses a Cellular Automaton to generate random numbers using Rule 30.

MATLAB 7.8.0 (R2009a) - 174 171 161 150 138 131 128 124 characters

Function syntax: (124 characters)

Here's the easier-to-read version (with unnecessary newlines and whitespace added for better formatting):

function l(f,N),
  b=char(importdata(f))>46;
  for c=1:N,
    b=~fix(filter2(ones(3),b)-b/2-3);
  end;
  dlmwrite('out.txt',char(b*42+46),'')

And here's how the program is run from the MATLAB Command Window:

l('in.txt',100)

Command syntax: (130 characters)

After a comment about calling functions with a command syntax, I dug a little deeper and found out that MATLAB functions can in fact be invoked with a command-line format (with some restrictions). You learn something new every day!

function l(f,N),
  b=char(importdata(f))>46;
  for c=1:eval(N),
    b=~fix(filter2(ones(3),b)-b/2-3);
  end;
  dlmwrite('out.txt',char(b*42+46),'')

And here's how the program is run from the MATLAB Command Window:

l in.txt 100

Additional Challenge: Tweetable GIF maker - 136 characters

I thought for fun I'd see if I could dump the output to a GIF file instead of a text file, while still keeping the character count below 140 (i.e. "tweetable"). Here's the nicely-formatted code:

function l(f,N),
  b=char(importdata(f))>46;
  k=ones(3);
  for c=1:N+1,
    a(:,:,:,c)=kron(b,k);
    b=~fix(filter2(k,b)-b/2-3);
  end;
  imwrite(~a,'out.gif')

Although IMWRITE is supposed

Java, 441... 346

• Update 1 Removed inner if and more ugliness
• Update 2 Fixed a bug and gained a character
• Update 3 Using lots more memory and arrays while ignoring some boundaries issues. Probably a few chars could be saved.
• Update 4 Saved a few chars. Thanks to BalusC.
• Update 5 A few minor changes to go below 400 and make it just that extra bit uglier.
• Update 6 Now things are so hardcoded may as well read in the exact amount in one go. Plus a few more savings.
• Update 7 Chain the writing to the file to save a char. Plus a few odd bits.

Just playing around with BalusC's solution. Limited reputation means I couldnt add anything as a comment to his.

class M{public static void main(String[]a)throws Exception{int t=3240,j=t,i=new Integer(a[1])*t+t;char[]b=new char[i+t],p={1,80,81,82};for(new java.io.FileReader(a[0]).read(b,t,t);j<i;){char c=b[j],l=0;for(int n:p)l+=b[j+n]/88+b[j-n]/88;b[j+++t]=c>10?(l==3|l+c==90?88:'.'):c;}new java.io.FileWriter("out.txt").append(new String(b,j,t)).close();}}

More readable(?) version:

class M{
 public static void main(String[]a)throws Exception{
  int t=3240,j=t,i=new Integer(a[1])*t+t;
  char[]b=new char[i+t],p={1,80,81,82};
  for(new java.io.FileReader(a[0]).read(b,t,t);j<i;){
    char c=b[j],l=0;
    for(int n:p)l+=b[j+n]/88+b[j-n]/88;
    b[j+++t]=c>10?(l==3|l+c==90?88:'.'):c;
  }
  new java.io.FileWriter("out.txt").append(new String(b,j,t)).close();
 }
}

PHP - 365 328 322 Characters.

list(,$n,$l) = $_SERVER["argv"];
$f = file( $n );
for($j=0;$j<$l;$j++){   
    foreach($f as $k=>$v){  
        $a[$k]="";      
        for($i=0;$i < strlen( $v );$i++ ){
            $t = 0;
            for($m=-1;$m<2;$m++){
                for($h=-1;$h<2;$h++){
                    $t+=ord($f[$k + $m][$i + $h]);
                }
            }
            $t-=ord($v[$i]);          
            $a[$k] .= ( $t == 494 || ($t == 452 && ord($v[$i])==88)) ?  "X" : "." ;
        }
    }
    $f = $a;
}       
file_put_contents("out.txt", implode("\n", $a )); 

I'm sure this can be improved upon but I was curious what it would look like in PHP. Maybe this will inspire someone who has a little more code-golf experience.

• Updated use list() instead of $var = $_SERVER["argv"] for both args. Nice one Don
• Updated += and -= this one made me /facepalm heh cant believe i missed it
• Updated file output to use file_put_contents() another good catch by Don
• Updated removed initialization of vars $q and $w they were not being used

R 340 chars

cgc<-function(i="in.txt",x=100){
    require(simecol)
    z<-file("in.txt", "rb")
    y<-matrix(data=NA,nrow=40,ncol=80)
    for(i in seq(40)){
        for(j in seq(80)){
            y[i,j]<-ifelse(readChar(z,1) == "X",1,0)
        }
        readChar(z,3)
    }
    close(z)
    init(conway) <- y
    times(conway)<-1:x
    o<-as.data.frame(out(sim(conway))[[100]])
    write.table(o, "out.txt", sep="", row.names=FALSE, col.names=FALSE)
}
cgc()

I feel it's slightly cheating to have an add in package that does the actual automata for you, but I'm going with it cos I still had to thrash around with matricies and stuff to read in the file with 'X' instead of 1.

This is my first 'code golf', interesting....