File 1:
one
two
three
four

File 2:
A
B
C
D
##</code><code>##

one[tab]A
two[tab]B
three[tab]C
four[tab]D
##</code><code>##

while (my $col1 = <FILE1>) {
    chomp $col1;
    my $col2 = <FILE2>;
    print "$col1\t$col2";
}

##</code><code>##

until(eof(ONE) and eof (TWO)) 
{
    my $one = <ONE>;
    my $two = <TWO>;
    $one ||= "";
    $two ||= "";
    chomp($one);
    chomp($two);
    print "$one\t$two\n";
}