Okay, w/o questioning the idea, some code comments:
Well #1, as always "use strict". You'll be busted 9 ways from Sunday here, but cleaning them up will help you alot. But:

foreach(@sites){
     $site=$_;
     # call the sub
     &getpages($site);
  }
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seems:

foreach my $site ( @sites) {
  &getpages($site);
}
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is a little smoother. You're doing some mixing of your subs and globals: if you open OUTFILE, print @data to it, you should close it. If @data is a global, it probably shouldn't be populated in a sub. It can be but it's not a great coding practice. Subs should work on local, er, "my" data structures and return anything that the main routine needs to use. As in, you're getpages is ref/using the global $site, not the param, so it'd be better as:

sub getpages{
  #  start timer
  my $t0 = [gettimeofday];
  #  get the page
  my $site = shift;
  get("$site");
  #  stop timer
  my $t1 = [gettimeofday];
  #  write the values
  my $elapsed = tv_interval $t0, $t1;
  &writevalues($elapsed);
  if($debug){
     print "Site $site took $elapsed seconds to load\n";
  }
}      # sub getpages
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and notice I took the comment off of your print (print STDERR might be better). That's why you have $debug, though *I* prefer using debug to set various levels so you can have it on for just the code locations you need as in:

if ( $debug > 10 ) {
  print STDERR "Site $site took $elapased seconds to load\n";
}
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Your writevalues should then "my $elapsed = shift;" - yes, seems a bit cumbersome, but it'll help make this a bit more readable to the next monk who's reading your code (of course, you'd add "return $elapsed;" to sub getpages). Hmm, writevalues also seems troubled by the same thing, I guess I'd have put getpages and writevalues in the foreach $site loop in the main rather than have getpages call writevalues. I'd initialize @data w/ the date/time (I think:$data[$[] = scalar localtime; would be one way to get what you want) *before* you started your foreach loop, skip the $space var and put it in your output loop, which'd be:

$data[$[] = scalar localtime;
foreach my $site (@sites){
       # call the sub
       my $elapsed_time = &getpages($site);
       push @data, writevalues($elapsed_time);
    }
open(OUTFILE,">>$datafile") || die "Cannot open $datafile :$!"; 
     foreach $data (@data) {
       print OUTFILE "$data ";
     }
     print OUTFILE "\n";
   close OUTFILE;
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As for the next part (whoof, I'm tired), well you should probably be sure $samples isn't zero, er.

a