The following performs as required, though the worst-case scenario can involve up to N(N-1)/2 domain comparisons. I hope you don't have more than a few thousand domains to do this with.

use strict;
use warnings;

my (%domains, @domains, @sets, $i, $j);

%domains = (
    'domain1.com' =>
        ['company1', 'contact1', 'address1', 'phone1', 'fax1', 'email1
+'],
    'domain2.com' =>
        ['company2', 'contact2', 'address2', 'phone1', 'fax2', 'email1
+'],
    'domain3.com' =>
        ['company3', 'contact3', 'address3', 'phone3', 'fax3', 'email3
+'],
    'domain4.com' =>
        ['company3', 'contact4', 'address4', 'phone3', 'fax1', 'email1
+'],
    'domain5.com' =>
        ['company5', 'contact5', 'address5', 'phone5', 'fax5', 'email5
+'],
    'domain6.com' =>
        ['company5', 'contact6', 'address6', 'phone6', 'fax6', 'email5
+']);

@domains = keys %domains;
while ($#domains > -1) {
    my @newset = shift @domains;
    for ($i = 0; $i <= $#newset; $i++) {
        for ($j = 0; $j <= $#domains; $j++) {
            push @newset, splice(@domains, $j--, 1)
                if compare($newset[$i], $domains[$j]);
        }
    }
    push @sets, \@newset;
}

for (@sets) {
    print join ' ', sort @$_; print "\n";
}

sub compare {
    my $d1 = $domains{$_[0]};
    my $d2 = $domains{$_[1]};
    my $c = 0;
    for (0..$#$d1) {
        return 1 if $d1->[$_] && $d1->[$_] eq $d2->[$_] && ++$c == 2;
    }
}
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