I have reformatted your code to make it more readable:

if ($data=~/(\D{3}) *?(\d{1,2}) *?(\d{4})/) {
    $month = $datehash{$1};
    $day=$2;
    if ($day=~/\d{1}/) {
        $day='0'.$day;
    } 
    $year=$3;
    $sortingdate=join '', $year, $month, $day;
}
[download]

Your regular expression is okay, as far as it goes. The error is in the formatting. The test $day=~/\d{1}/ will match every one- or two-digit day specification, so you will always add a zero. Also, do the values of %datehash have leading zeroes where required? Here is how I would re-write your code:

my %datehash;
@datehash{ qw( Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec) } =
    map sprintf( '%02d', $_), 1 .. 12;

my $mon_re = join '|', keys %datehash;

while ( <DATA> ) {
    my ( $mon, $day, $year) = /($mon_re)\s+(\d\d?)\s+(\d{4})/;
    $day = sprintf '%02d', $day;
    print "$year$datehash{ $mon}$day\n";
}


__DATA__
Oct 16 2004 11:09:19:943AM
Mar 3 2007 10:30:31:170PM
[download]

I have made the regular expression more specific for the month names (since %datehash is already there) and less specific for white space (allowing any, not only blanks).

Anno