I'd probably select Time::Local there. There's a gotcha or two to lookout for though.

my ($S, $M) = (0,0);
my $H = $1 if $hour =~ m/0*(\d+)/; # I'm not sure if leading 0s hurt
my $d = $1 if $day =~ m/0*(\d+)/;
my $m = $1 if $month =~ m/0*(\d+)/;
   $m --; # gotcha!  the month is 0-11

# timelocal($sec,$min,$hour,$mday,$mon,$year);
my $utime = timelocal($S, $M, $H, $d, $m, $year);
[download]

Although, in general, Date::Manip is the way to go, timelocal is a million times faster.

Not exactly answering your question maybe…
…but since your time string is perfect for pulling the time comparison into the domain of string comparison…

use strict;
use warnings;

chomp(my @directories_time_tagged = <DATA>);

for my $directory_name ( @directories_time_tagged ) {
  next unless $directory_name =~ /(\d\d\d\d_\d\d_\d\d_\d\d)/;  # Year_
+month_day_hour
  my $date_time = $1;
  my ($year, $month, $day, $hour) = split /_/, $date_time;

  my ($y_now, $m_now, $d_now, $h_now) = (localtime)[5,4,3,2];

  my $now = sprintf('%d_%02d_%02d_%02d', $y_now+1900, $m_now+1, $d_now
+, $h_now);

  if ($date_time le $now ) {  # If the date has been passed
    print "\nconditions have been met for $directory_name\n";
  }
}

__DATA__
foo_2006_03_02_14_verzeichnis
bar_2007_05_02_02_directory
baz_2007_05_03_22_dossier
[download]

Just a nitpick: I don't think you need to reassign a value to $now on every iteration of the loop.

I like this code because it takes out the need for a module. The wider context for the code you have given me is:

my (@priority_numbers_in_order, @directories_to_transport) = Search_di
+rectories ($input_directory_C, $node);


my $count = 0;

for (@directories_to_transport){

  my $priority_number = $priority_numbers_in_order[$count];

  my $specific_recipient_directory = "$recipient_directory"."$priority
+_number";

  $dir = $_;

  opendir(DIR, "$dir") or die $!;

  my $file_name;

  while (<DIR>){
    $file_name = $_;
  }


  my $dir_and_filename = $dir.$file_name;

  rename "$dir_and_filename", "C:$specific_recipient_directory/$file_n
+ame" or warn $!;

  $count++;

}




sub Search_directories {

  my ($input_directory_CC, $node) = @_;

  my $directory_of_interest = "$input_directory_CC";

  opendir (DIRY, "$directory_of_interest") or die "Error opening direc
+tory : $!";

  my @directories;

  while ($_ = (readdir DIRY)) {

    print $_, "\n";

    if (-d "$input_directory_CC/$_") {
      print "This is a dir $_ \n";

      if ($_ =~ /\d$/){   
    print "This directory is a number: $_";
    push (@directories, $_);
      }
    }
  }
  close DIRY;

  print "\n\&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n".$input_directory_CC.@dire
+ctories."\n\n";



  for my $dir_num (@directories)
    {
      my @direcories_to_transport;

      print "\nforeach of the direcotories : $dir_num\n";
      my $input_dir = $input_directory_CC.$dir_num;
      print ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>$input_dir";
 
      opendir DIRY, $input_dir or die "Error opening directory $input_
+dir - $!";
 
      my @directories_time_tagged =
    grep /\d*$/,
      readdir DIRY;

      closedir DIRY;

      chomp(my @directories_time_tagged = <DATA>);
 
      for my $directory_name ( @directories_time_tagged ) {
    next unless $directory_name =~ /(\d\d\d\d_\d\d_\d\d_\d\d)/;  # Yea
+r_month_day_hour
    my $date_time = $1;
    my ($year, $month, $day, $hour) = split /_/, $date_time;
    
    my ($y_now, $m_now, $d_now, $h_now) = (localtime)[5,4,3,2];
    
    my $now = sprintf('%d_%02d_%02d_%02d', $y_now+1900, $m_now+1, $d_n
+ow, $h_now);
    
    if ($date_time le $now ) {  # If the date has been passed
      print "\nconditions have been met for $directory_name\n";

      my $directory_to_move = $input_directory_CC.$dir_num..$directory
+_name;
    
      push (@direcories_to_transport,  $directory_to_move);
      push (@priority_numbers_in_order, $dir_num);

    }
      }
    }
  return @priority_numbers_in_order, @direcories_to_transport;
}
[download]

I've not tested it though.

use strict;
use warnings;
use DateTime;

my @dirs = ...

DIR: for my $dir (@dirs) {
    next DIR if (!($dir =~ /(\d{4})_(\d{2})_(\d{2})_(\d{2})/));
    my $dir_time = DateTime->new( year => $1,
                                  month => $2,
                                  day => $3,
                                  hour => $4, 
                                  time_zone => 'floating',
                                );
    if (0 <= DateTime->compare($dir_time, DateTime->now(time_zone => '
+floating')) {
        print "whatever\n";
    }
}
[download]

A sensible first step (suggested in what is left hanging at the end of your code) is to convert the current time to a format that matches the directories, before doing anything with them at all (i.e. why read them into an array unfiltered - put all the filtering in one place and process in a grep/readdir loop without needing an array...)

Update: added comments in Filter subroutine as requested by OPer

# convert current time to same format as dirs
my $now;
{ my @now = localtime();
  $now = $now[5]+1900;
  $now[4]++;
  for ( my $i = 4; $i > 1; $i-- ) {
    $now .= '_';
    $now[$i] = "0$now[$i]";
    $now[$i] = substr( $now[$i], -2 );
    $now .= $now[$i];
  }
}
# get only those directories that match requirements:
my $dir = "parent-of-directories";
opendir my $dh, $dir or die $!;
for my $file ( grep Filter( now => $now, dir => $dir ), readdir $dh ) 
+{
   my $path = "$dir/$file";
   # and go right ahead and process the directory "$path" here in the 
+loop
   # ...
   #
}
closedir $dh;

sub Filter { # put all filter conditions here ...
    my %opt = @_;

    ( -d "$opt{ dir }/$_" )   # is a directory
      && !/^\./               # is also not hidden/special
      && /(\d{4}_\d{2}_\d{2}_\d{2})/
                              # contains date/hour
      && ($opt{ now } gt $1 ) # that is in the past
      ; 
}
[download]