Now I think I should say that I am not aware of any compiler that will compile code with nested comments, so this is probably not a big problem.

However I played around and this seems to do the trick: (just replace the while loop in my code above with this one.)

while( $file =~ /\Q$start\E(.*?)\Q$end\E/sg )
{
    $a = $1;
    $match = $&;
    
    #look for more start tags in what we matched 
    while( $a =~ /\Q$start\E/sg )
    {
        #balance the ending comments
    $file =~ /.*?\Q$end\E/sg;    
        $match .= $&;
    }
    print $match, "\n";
}
[download]

For your tests file I got what you wanted.

For other tests I used this test.txt:

blah blah
/* comment 1 */

blah blah
/* comment 2 */
blah blah
/*  outer 
    /* 
        mid
            /*
                center
            */
        mid  
    */ 
    outer 
*/
[download]

And here are my results:

prompt$ regex.pl '/*' '*/'
/* comment 1 */
/* comment 2 */
/*  outer
    /*
        mid
            /*
                center
            */
        mid
    */
    outer
*/
[download]

So enjoy this fanciful result.

I hope this helps.