I'm almost embarressed to submit this (it's very dirty as far as I can tell), but here is my go:

#!/usr/bin/perl  
 
use strict; 
 
sub readfile { 
  my $fn=shift; 
  my @ar; 
 
  open IN,"<$fn" || die "Couldn't open '$fn': $!"; 
  ## snarf the header 
  scalar <IN>; 
  ## read the rest 
  while (<IN>) { 
    chomp; 
    push @ar,$_; 
  } 
  close IN; 
 
  @ar; 
} 
 
## load the files into arrays 
my @a=readfile '1'; 
my @b=readfile '2'; 
my @c=readfile '3'; 
 
## iterate until all arrays are empty 
while (defined @a || defined @b || defined @c) { 
  ## find the lowest value 
  my $s; 
  $s=$a[0] < $b[0] ? $a[0] : $b[0]; 
  $s=$s < $c[0] ? $s: $c[0]; 
 
  ## print them out (if they match) 
  printf "%5s", $a[0]==$s ? scalar shift @a : undef; 
  print " | "; 
  printf "%5s", $b[0]==$s ? scalar shift @b : undef; 
  print " | "; 
  printf "%5s", $c[0]==$s ? scalar shift @c : undef; 
 
  print "\n"; 
}
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What i don't like about this: I don't like the selection of the next value (the assignment to $s). It does, however, allow for non-linear data (you can have 1,2,3,4 in one file, 2,3,10 in another and 66 in the third and it will still work).