McA,
My brain is mush so unfortunately, this critique is just the things that jumped out at me. 
%alphabet = (%alphabet, map { $_ => 1 } @chars);

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Would be better written as: 
@alphabet{@chars} = (); # No need to set values to 1 as you only ever 
+use keys

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I am not sure why you avoid autovivication but 

    if(defined $sorted{$characters}) {
        push @{$sorted{$characters}}, $line;
    }
    else {
        $sorted{$characters} = [$line];
    }

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Would work just as well as: 
push @{$sorted{$characters}}, $line;

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You waste a lot of time going through loops that you abort early 
    foreach (my $pos2 = 0; $pos2 < $count; $pos2++) {
        next if $pos2 < $pos1;

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Would work a lot more efficiently as: 
for (my $pos2 = $pos1; $pos2 < $count; $pos2++) {

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I haven't tested it but the way you determine if one is a subset of the other would probably be better as subtracting one hash from another.

Cheers - L~R

In reply to Re^11: Challenge: 8 Letters, Most Words by Limbic~Region
in thread Challenge: 8 Letters, Most Words by Limbic~Region

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