use Data::Dumper;

# get you datafile into a scalar variable (sample put in __DATA__)
my $data = join '', <DATA>;

my $split_pat = qr/-{28}\n([\w\d\.-]+)\n-{28}\n*/;
my @data = split /$split_pat/, $data;
shift @data;
%servers = @data;

for my $server (keys %servers) {
    my %progs = split /\n{2,}/, $servers{$server};
    $servers{$server} = \%progs;
    for my $prog ( keys %{$servers{$server}} ) {
        my @data = split /\n+/, $servers{$server}->{$prog};
        $servers{$server}->{$prog} = \@data;
    }
}

print Dumper \%servers;

__DATA__
Dumper output:

$VAR1 = {
          'Server1.dom.com' => {
                                 'WINDOWS 2000 SERVER SP2' => [
                                                                'WARNING MS01-022 Q296441',
                                                                'Patch NOT Found MS02-001 Q311401',
                                                                'Patch NOT Found MS02-006 Q314147',
                                                                'Patch NOT Found MS02-012 Q313450',
                                                                'Patch NOT Found MS02-013 Q300845',
                                                                'Patch NOT Found MS02-014 Q313829'
                                                              ],
                                 'Internet Information Services 5.0' => [
                                                                          'Patch NOT Found MS02-001 Q311401',
                                                                          'Patch NOT Found MS02-012 Q313450'
                                                                        ],
                                 'Internet Explorer 5.5 SP2' => [
                                                                  'Patch NOT Found MS02-005 Q316059',
                                                                  'Patch NOT Found MS02-009 Q318089'
                                                                ]
                               },
          'Server2.dom.com' => {
                                 'WINDOWS 2000 SERVER SP2' => [
                                                                'WARNING MS01-022 Q296441',
                                                                'Patch NOT Found MS02-001 Q311401',
                                                                'Patch NOT Found MS02-006 Q314147',
                                                                'Patch NOT Found MS02-013 Q300845',
                                                                'Patch NOT Found MS02-014 Q313829'
                                                              ],
                                 'Internet Explorer 5.5 SP1' => [
                                                                  'Patch NOT Found MS02-005 Q316059',
                                                                  'Patch NOT Found MS02-009 Q318089'
                                                                ]
                               }
        };