Here's my version (hash of hash):

#!/usr/bin/perl
use strict;

my %data_by_employee;
my %data_by_form;

# read in tab-delimited data fields into
# two hashes-of-hashes (actually, two hashes of hash refs)
while(my $line = <DATA>) {
  chomp $line;
  my ($employee, $form, $date) = split(/\t/,$line);
  next unless ($employee && $form && $date); # skips blank lines

  $data_by_employee{$employee}{$form} = $date;
  $data_by_form{$form}{$employee} = $date;
}

print "By Employee:\n";
for my $employee (sort keys %data_by_employee) {
  print "$employee\n";
  # note: $data_by_employee{$employee} is a hash reference,
  # so we have to dereference it by using %{ }
  for my $form (sort keys %{ $data_by_employee{$employee} } ) {
    my $date = $data_by_employee{$employee}{$form};
    print "\t$form\t$date\n";
  }
}
print "\n";

print "By Form:\n";
for my $form (sort keys %data_by_form) {
  print "$form\n";
  # note: $data_by_form{$form} is a hash reference,
  # so we have to dereference it by using %{ }
  for my $employee (sort keys %{ $data_by_form{$form} } ) {
    my $date = $data_by_form{$form}{$employee};
    print "\t$employee\t$date\n";
  }
}
print "\n";

__DATA__
10001   10      20090101
10002   10      20080515
10003   10      20090323
10001   20      20090412
10002   20      20090711
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