This is just the thing hashes exist for:

#Untested
use strict;
my %data;
#assume file is opened as <INPUT>
while (<INPUT>) {
  chomp;
  my ($server,@apps_info)=split /,/;
  push @{$data{$server}}, \@apps_info;
}
foreach my $server ( keys %data ) {
  print "$server\n\t";
  for ( @{$data{$server}} ) {
    print join " ", split /,/;
    print "\n\t";
  } 
}
[download]

Basically, pull all of the data into a hash with the server name as keys.

Update: Updated as per Tomtom's remark