First of all change

while (<TEST>) {
  my ($key,@fileData) = split /\|/;
  chomp @fileData;
  $test{$key} = \@fileData;
}
#to
while (<TEST>) {
  chomp;
  my ($key,@fileData) = split /\|/;
  $test{$key} = \@fileData;
}
[download]

Otherwise you are chomping every item in the array, when you know there can only be a newline at the end of the line.

I would change

foreach my $key (keys %test) {
      push (@sorted, "$key|$test{$key}->[0]|$test{$key}->[1]|$test{$ke
+y}->[2]|$test{$key}->[3]");
}
#to 
foreach my $key (keys %test) {
      push @sorted, (join '|', ($key,@{$test{$key}});        
}
[download]

except that that is overkill... since you can't have the multiples of the same key, you don't need to sort on the whole line, just the key, I would do...

open(TEST, ">test.txt") || die "File couldn't be opened for writing: $
+!";
foreach my $key (sort keys %test) {
  print TEST (join '|', ($key,@{$test{$key}});
  print TEST "\n";
} 
close(TEST);
[download]

Instead of the whole @sorted thing

Update Sorry, you wanted to sort by the last item in the array of data... change

foreach my $key (sort keys %test) {
#to
foreach my $key (sort { $test{$a}[-1] <=> $test{$b}[-1] } keys %test) 
+{
[download]

the $test{$a}[-1] <=> $test{$b}[-1] sorts numerically based on the final item in the data array at each key
Untested, but I believe it all works fine

                - Ant