Easy.

use Modern::Perl;
use Data::Dump qw/dump/;

my %database;

while (<DATA>) {
    next if /^#/;
    chomp;
    my (undef, $ip, $rw, $amount, $file) = split /,\s?/;
    $database{$ip}{$rw}{$file} += $amount;
}

say dump(\%database);

__DATA__
#
##DATE  IP Write/Read TransferData FileName
#
Sun Aug 21 12:08:21 2011,172.22.32.28, W, 4964,/export/file1.log
Sun Aug 21 12:08:21 2011,172.22.32.28, W, 4964,/export/file2.log
Sun Aug 21 12:08:21 2011,172.22.32.28, W, 4963,/export/file2.log
Sun Aug 21 12:08:21 2011,172.22.112.141, W, 9292,/export/home/another.
+file
Sun Aug 21 12:08:21 2011,172.22.32.28, W, 4964,/export/file2.log
Sun Aug 21 12:08:21 2011,172.22.32.28, W, 2493,/export/file1.log
Sun Aug 21 12:08:21 2011,172.22.32.28, W, 2355,/export/another.log
Sun Aug 21 12:08:21 2011,172.20.220.38, W, 3699,/export/file2.log
Sun Aug 21 12:08:21 2011,172.20.220.146, W, 1996,<?>
Sun Aug 21 12:08:21 2011,172.22.32.28, W, 2776,/export/file1.log
[download]

output:

{
  "172.20.220.146" => { W => { "<?>" => 1996 } },
  "172.20.220.38"  => { W => { "/export/file2.log" => 3699 } },
  "172.22.112.141" => { W => { "/export/home/another.file" => 9292 } }
+,
  "172.22.32.28"   => {
                        W => {
                               "/export/another.log" => 2355,
                               "/export/file1.log"   => 10233,
                               "/export/file2.log"   => 14891,
                             },
                      },
}
[download]

Caution: this script does not perform any checking whether the data is in a valid format! For instance, your 4th data-line is in a "wrong" format which I assume is just a typo and I "corrected" it by hand.

Printing the results in a pretty format is left as an exercise for the reader.