my $string = qq~
GENLIST    =  Array2.genlist                   # Kommentar
TERMLIST  =  02_IrgendeineListe   03_IrgendeineListe           # Kommentar      \
                                               # Kommentar,    \
                                               # Kommentar
STARTLIST    = dateiname.ids                   # Kommentar
OUTPUTNAME =                                   # Kommentar
CROSSLIST    = 01_XY                           # Kommentar
ADDFILTER  =                                   # Kommentar
~;

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

my %hash;


my @lines = split /\r?\n/,$string;
for (@lines) {
  if (/(\w+?)\s*?=\s*?(.*?)#/) {
    my ($key,$values) = ($1, $2);
    my @values = $values =~ /\s*(\S+)\s*/g;
    $hash{$key} = [@values];
  }
}

print Dumper \%hash;
_ _ END _ _
$VAR1 = {
          'ADDFILTER' => [],
          'CROSSLIST' => [
                           '01_XY'
                         ],
          'TERMLIST' => [
                          '02_IrgendeineListe',
                          '03_IrgendeineListe'
                        ],
          'OUTPUTNAME' => [],
          'STARTLIST' => [
                           'dateiname.ids'
                         ],
          'GENLIST' => [
                         'Array2.genlist'
                       ]
        };