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foreach my $software (keys %bad_stuff) {
    if($subkey =~ $bad_stuff{$software}) {
...
        print "Machine $machine could have $software installed\n";
    }
}

foreach my $subkey ($user_key->SubKeyNames,$software_key->SubKeyNames)
+ {
     if ( exists $bad_stuff{$subkey} ) {
...
     }
                         
}