open( LINKS, "+<", "filename" );
while (<LINKS>) {
   my $lastread = tell LINKS;  # keep track of where you are
   seek LINKS, 0, 2;  # jump to end-of-file
   ...
   # do stuff with current value of $_, including:
   print LINKS "another line of data\n";
   ...
   # when all done adding updates at the end...
   seek LINKS, $lastread, 0; # jump back for next read:
}

##</code><code>##

   ...
   next if exists( $fetched{$url} );
   ...

##</code><code>##

while (-s "list1") {
   open( INP, "<list1" ) or die $!;
   open( OUT, ">list2" ) or die $!;
   while (<INP>) {
      chomp;
      (my $pagefile = $_ ) =~ s{[ \\/?&#!;]+}{_}g; # transform url into a safe file name
            # (update: added backslash to the character set)

      next if ( -e $pagefile );  # skip if we already have it
      ...
      # fetch the page, extract links if any
      ...
      foreach $link ( @links ) {
         ...
         # work out the full url
         ...
         print OUT $url, "\n";
      }
      open PAGE, ">$pagefile";  # save current page to its own file
      print PAGE $content;
      close PAGE;
   }
   close INP;
   close OUT;

   system( "sort -u list2 > list1" ); # rewrite list1 with only the unique strings in list2
}

print "list1 is empty now.  We must be done.\n";