Sort::Key::Natural perhaps?

Anyway, here's my try. I did not check thoroughly, but it seems to work.

sub natural_sort {
    my $idx = shift || 0;
    return -1 if !defined $a->[$idx];
    return  1 if !defined $b->[$idx];

    if ($a->[$idx] =~ /^[0-9]/ and $b->[$idx] =~ /^[0-9]/) {
        $a->[$idx] <=> $b->[$idx] or natural_sort($idx + 1);
    } else {
        $a->[$idx] cmp $b->[$idx] or natural_sort($idx + 1);
    }
}

my @files = <DATA>;

print for
    map { join "", @$_ }
    sort natural_sort
    map { [ split /(\d+)/, $_  ] } @files;

__DATA__
abcd1_abc_123456.abc1a_A.201307290800-0900-0.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-1.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-10.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-11.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-2.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-3.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-0.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-1.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-10.gz
abcd1_abc_123456.abc1a_A.201305290800-0900-11.gz
abcd1_abc_123456.abc1a_A.201308290800-0900-2.gz
abcd1_abc_123456.abc1a_A.201302290800-0900-3.gz
abcd1_abc_123456.abc1a_A.201306290800-1000-1.gz
abcd1_abc_123456.abc1a_A.201306290800-1000-10.gz
abcd1_abc_123456.abc1a_A.201305290800-1000-11.gz
abcd1_abc_123456.abc1a_A.201308290800-1000-2.gz
abcd1_abc_123456.abc1a_A.201302290800-1000-3.gz
[download]