My original best was 63 characters: 
sub canonical {
my(@a,$i,%c,$c)=pop=~/./g;$c.=$c{$_}||=$a[$i++]for pop=~/./g;$c
}

[download]
(which is strict compliant, but only because at that point it wasn't any shorter being non-strict compliant. :)

However, here's a 46 character solution building off of btrott's solutions: 

sub canonical {
($_,$a,%h)=@_;s!.!$h{$&}||=($a=~/./g,$&)!ge;$_
}

[download]
Can be called multiple times, of course, as in the example.

 

Update: Well, tilly's been mumbling something about following the spec :) , so here's a solution that accepts any ASCII character (including zero and linefeed) in the word or the alphabet: 
sub canonical {
($_,$a,%h)=@_;s!.!{$h{$&}=~s+^\z+$a=~/./gs,$&+ge}$h{$&}!gse;$_
}

[download]
At 62, it actually beats my original solution by 1 character!

In reply to Re: (Golf) Cryptographer's Tool #1 by chipmunk
in thread (Golf) Cryptographer's Tool #1 by Masem

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