#!/usr/bin/perl -w
use strict;

my @files = qw(file1.dat file2.dat file3.dat);
my %hash;

foreach my $file (@files)
{
   open (FILE, "<", $file) || die "can't open $file $!";
   while (<FILE>)
   {
      next if /^\s*$/;  #simply skips blank lines
      chomp;
      my ($name,@tokens) = split(/,/,$_);
      $name =~ s/_ref\d+$//; 
      push @{$hash{$name}},@tokens;
   }
}

foreach my $name (sort keys %hash)
{
   print "$name  @{$hash{$name}}\n";
}

__END__
prints:
aaa_1  4 5 8 9
bbb  2 3 5 10
ccc_1  5 6 6 11