добавить перенос строки...

<?php

set_time_limit(0);

$file = nl2br(file_get_contents('2.txt'));

preg_match_all('/\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}/',$file,$matches);
foreach ($matches as $key=>$value)
{  
    $count = count($value);
    for($q=0;$q<$count;$q++)
    {
    $file1[]=trim($value[$q]);
    }
}
$result = array_unique($file1);
foreach ($result as $key=>$text)

$file = 'sort.txt';
file_put_contents($file,$result );

?>
</body>
</html>

<?php

set_time_limit(0);

$file = nl2br(file_get_contents('2.txt'));

preg_match_all('/\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}/',$file,$matches);
foreach ($matches as $key=>$value)
{  
    $count = count($value);
    for($q=0;$q<$count;$q++)
    {
    $file1[]=trim($value[$q]) . "\n";
    }
}
$result = array_unique($file1);
foreach ($result as $key=>$text)

$file = 'sort.txt';
file_put_contents($file,$result );

?>
</body>
</html>