Note that your sample output is wrong. If going from 4 to 4 changes 0%, than going from 6 to 8 should change 33%, not 133%. Also, you cannot express the change going anywhere from 0.

You might find the following code useful. I have modified some values to show some other interesting results.

#!/usr/bin/perl
use warnings;
use strict;

my %hash = (
            file1 => {
                      foo    => 4,
                      bar    => 6,
                      baz    => 4,
                      quux   => 8,
                      quuux  => 6,
                      quuuux => 0,
                     },
            file2 => {
                      foo    => 4,
                      bar    => 8,
                      baz    => 4,
                      quux   => 8,
                      quuux  => 5,
                      quuuux => 0,
                     },
            file3 => {
                      foo    => 8,
                      bar    => 0,
                      baz    => 5,
                      quux   => 8,
                      quuux  => 5,
                      quuuux => 3,
                     },
           );

my %columns = map { $_ => 1 } map keys %{ $hash{$_} }, keys %hash;
my @files = qw/file1 file2 file3/;

for my $column (keys %columns) {
    print $column, "\t", $hash{$files[0]}{$column};

    for my $i (1 .. $#files) {
        my ($this, $previous) = map $hash{ $files[$_] }{$column}, $i, 
+$i - 1;
        print "\t", $this;

        my $change = '-';
        if ($previous) {
            $change = sprintf "%d%%", 100 * ($this - $previous) / $pre
+vious;
        }
        print "\t$change";
    }
    print "\n";
}
[download]

Output:

bar     6       8       33%     0       -100%
baz     4       4       0%      5       25%
quuux   6       5       -16%    5       0%
quux    8       8       0%      8       0%
foo     4       4       0%      8       100%
quuuux  0       0       -       3       -
[download]