Something like this might be what you're looking for:

#! perl -slw
use strict;

sub common {
    die 'Bad args' unless @_ == 2;
    my $output = $_[ 0 ] ^ $_[ 1 ];

    $output =~ s[([^\0]+|[\0]+)]{
        my $p = $-[0];
        my $l = $+[0] - $-[ 0 ];
        ord( $1 ) == 0
            ? substr( $_[ 0 ], $p, $l )
            : join '', map{ '[' . substr( $_, $p, $l ) . ']' } @_
    }ge;
    return $output;
}

while( my $str1 = <DATA> ) {
    my $str2 = <DATA>;
    print common( $str1, $str2 );
}

__END__
a11211b123
a11222b123
The quick brown fox jumps over the lazy dog
the quiet green fir looms over the lazy dog
Send reinforcements; we're going to advance
Send 3 and sixpence; we're going to a dance
Time flies like an arrow
Dung flies like a  brick
[download]

Output:

c:\test>junk1
a112[11][22]b123

[T][t]he qui[ck][et] [b][g]r[ow][ee]n f[ox][ir] [jump][loom]s over the
+ lazy dog

Send [rei][3 a]n[forcem][d sixp]en[ts][ce]; we're going to a[dv][ d]an
+ce

[Time][Dung] flies like a[n][ ] [a][b]r[row][ick]
[download]

Not sure about the usefulness of the output format though.