use Text::Soundex 'soundex';

my @words = qw(
  Cow     Phone
  Speaker Phone
  Hello   World
  Phon    Speaker
  Clock   Phon
  Torld   Hello
  Hello   Worlx
);

while( @words ) {
  push @pairs, [ shift @words, shift @words ];
}

@pairs = map { $_->[1] } 
         sort { $a->[0] cmp $b->[0] } 
         map {
           [ join( '' => sort { $a cmp $b } 
                     ( soundex @$_[0], soundex @$_[1] ) ),
             $_ 
           ] } @pairs;

for( @pairs ) {
  print "@$_\n";
}
[download]

output:

Cow Phone
Clock Phon
Torld Hello
Hello World
Hello Worlx
Speaker Phone
Phon Speaker
[download]

Update: I've chosen soundex just because it was very easy to implement.
Other string comparison methods might give better/more exact results.