Consider using a "here document"

use strict;
use warnings;

my @names = qw(file1 file2);

for my $name (@names) {
    my $fil;
    open $fil, '>', "$name.ini";
    print $fil <<END
[main]
left_hand_side=$name.html
right_hand_side=$name.php
file_regex_pattern=\\.php\$
dir_regex_pattern=(?!^svn\$)
END

}
[download]