If the rows are in any given order you could exploit that. If not then if you first sorted them with

tail +2 d1.dat > d1.sorted
tail +2 d2.dat > d2.sorted
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The tail +2 just removes the header line from each. You can then merge them with

open(D1,"<d1.sorted");
open(D2,"<d2.sorted");

my $d1 = "v1 v2 v3";
my $d2 = "t1 t2 t3";
my ($d1k,$d2k)=('','');

for(;;) {
  my $c = $d1k cmp $d2k
    or print join(" ", split(/\s+/,$d1), (split(/\s+/, $d2))[2]),"\n";

  if ($c <= 0) {
    last unless defined($d1 = <D1>);
    $d1k = ($d1 =~ /^(\d+\s+\d+)/)[0];
  }

  if ($c >= 0) {
    last unless defined($d2 = <D2>);
    $d2k = ($d2 =~ /^(\d+\s+\d+)/)[0];
  }
}
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It'll take a long time, but do something like

my %firstDataSet;
foreach (my $line = <FIRST_FILE>) {
    my @data = split /\s+/, $line;
    $hash{$data[0]}{$data[1]} = $data[2];
}

foreach (my $line = <SECOND_FILE>) {
    my @data = split /\s+/, $line;
    if ($hash{$data[0]}{$data[1]}) {
        print OUT_FILE "$data[0] $data[1] $hash{$data[0]}{$data[1]} $d
+ata[2]\n";
    }
}
[download]

------
We are the carpenters and bricklayers of the Information Age.

Don't go borrowing trouble. For programmers, this means Worry only about what you need to implement.

With 500MB files, I'd consider MLDBM if I were to go this route. What I'd probably do (if its an option for the OP) is stick with unix utilities (I'm assuming the fields are space delimited, and you don't mind sorted results):

sed 's/ /|/' file1 | sort >tmp1
sed 's/ /|/' file2 | sort >tmp2
join tmp1 tmp2 | sed s/|/ /' > result
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If both files are 500M you probably don't want to read them all into memory to work on them (unless you've got over a gig of RAM and/or swap handy). If you know that lines in the different files are always going to match up (line 25 in file one always corresponds to line 25 in file two):

open( ONE, "file1" ) or die "open file1: $!";
open( TWO, "file2" ) or die "open file2: $!";
open( OUT, ">merged" ) or die "open merged: $!";

while( <ONE> ) {
  chomp;
  my $two = <TWO>;
  print OUT $_, (split( " ", $two ))[-1], "\n"
}

close( ONE ); close( TWO ); close( OUT );
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If you can't guarantee a one-to-one mapping between lines, then you probably want to look into using DB_File or the like to generate a hash on disk of the second file key'd by the first two columns (assuming that's what relates the values from the two different files). Then you'd read through the first file and pull the corresponding value from the hash.

Since you mention Stata, SAS and awk, a non-perl solution's acceptable? Since you've got awk, you're on a unix system? Are you aware of join?

Caveats: the files must be sorted, and it'll only join on one field, so you'ld need to prepare the files:

tail +2 d1.dat | sort | sed 's/ /:/' > d1.sorted
tail +2 d2.dat | sort | sed 's/ /:/' > d2.sorted
join d1.sorted d2.sorted | sed 's/:/ /'
[download]

And anyway, it never hurts to know about something else perl can render obsolete ;-)