#!/usr/bin/perl

use strict;
use File::Find;

my $dir = shift;
if (!$dir) {die "perl $0 [startdir]\n";}
my @subdirs = ();
my $subdirsRef = \@subdirs;
my %size;

&get_sub_dirs($dir, $subdirsRef);

for my $foo (@subdirs) {
   $size{$foo} = (&dir_tree_size($foo));
}

print "Subdirectory size report for $dir\n\n\n";
foreach my $key (sort keys %size) {
   print "$key = ";
   printf("%.3f", $size{$key});
   print " K\n";
}
print "\n\n";
sub get_sub_dirs {
   my ($dir, $arrayRef) = @_;
   opendir DIR, $dir;
   my @files = grep !/^\.\.?$/, readdir DIR;
   for my $i (@files) {
      if (-d $i) {
         push @$arrayRef, $i;
      }
   } 
}

sub dir_tree_size {
   my $dir = shift;
   my ($i,$total);
   $total = 0;
   opendir DIR, $dir;
   my @files = grep !/^\.\.?$/, readdir DIR;
   for $i (@files) {
      if(-d $dir . "\\" . $i) { 
     $total += &dir_tree_size($dir . "\\$i") 
       } else { $total += -s $dir . "\\" . $i}
   }
   $total = $total / 1024;
   return $total;
}
[download]

Why are you useing File::Find if you're not actually using it? Your code could be reduced a lot if you used File::Find, and your code would be able to safely handle symlinks and other operating systems.

If your behavior was a little simpler (relying on arguments instead of finding subdirs first):

use File::Find;
use strict;

foreach my $dir (@ARGV) {
   my $total;
   find(sub { $total += -s }, $dir);
   print "$dir: $total\n";
}
[download]

Preserving the behavior of your script (mostly):

use File::Find;
use File::Spec;
use strict;

my $cur = File::Spec->curdir;
my $up  = File::Spec->updir;

foreach my $start (@ARGV) {
   my @dirs = &find_subdirs($start);

   foreach my $dir (@dirs) {
      my $total = 0;
      find sub { $total += -s }, $dir;
      printf "%-20s %d\n", $dir, $total;
   }

   print STDERR "$start: No subdirectories\n" unless @dirs;
}

sub find_subdirs {
   my $start = shift;

   unless(opendir(D, $start)) {
      warn "$start: $!\n";
      next;
   }

   my @dirs =
      map {
          -d "$start/$_" &&
         !-l "$start/$_" &&
         $_ ne $cur && $_ ne $up
            ? "$start/$_" : ()
      }
      readdir(D);

   closedir(D);

   @dirs;
}
[download]

The reason the File::Find is in there is because I put that script together from a couple of others I was working with, and the use got left in there on accident.