my $arrayIndex = 0;
my $blocks;

open(IN,'<',$inputFile)
  or die "Fehler beim Oeffnen von $inputFile: $!\n";

while ( my $line = <IN>) {
  chomp($line);

  # Neuer Block? Dann Index hochzaehlen
  if ($line =~ /^#/) {
    $arrayIndex++;
  }
  else {
    push(@{$blocks->[$arrayIndex]}, $line);
  }
}

close(IN);
...

#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

my @blocks;

{
    local $/ = "#\n";
    while(my $entry = <DATA>){
        chomp $entry;
        push @blocks,$entry;
    }
    
    @blocks = grep{$_}@blocks;
}

print Dumper(\@blocks);

__DATA__
#
   dlf951121.1200.n2.txt
   dlf951121.1230.n2.txt
   dlf951121.1330.n4.txt
#
   dlf951121.1200.n2.txt
   dlf951121.1230.n2.txt
   dlf951121.1330.n4.txt
#
   dlf951121.1200.n2.txt
   dlf951121.1230.n2.txt
   dlf951121.1330.n4.txt
#
   dlf951121.1200.n6.txt
   dlf951121.1230.n4.txt
#
   dlf951121.1200.n6.txt
   dlf951121.1230.n4.txt
#

my @data;
open(DATEN, 'meine.daten');
{
  local ($/) = "#\n";
  @data=<DATEN>;
 chomp(@data);
}
close(DATEN);

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $listfile='/pfdad/zur/datei.txt';
my @liste=();

open(FILE,'<', $listfile) or die "Konnte $listfile nicht oeffnen ($!)\n";
{
  local $/="#\n";
  push(@liste,[split(/\n/,$block)]) while(my $block=<FILE>);
}
close(FILE);
print Dumper(\@liste);