#!/usr/bin/perl -w
use strict;
use HTML::TokeParser;

my $sample_HTML = 
  "<a href=\"http://www.foobar1.com/\">link 1</a> " .
  "<!--ignore--><a href=\"http://www.foobar2.com/\">link 2</a> " .
  "<a href=\"http://www.foobar3.com/\">link 3</a> ";

my $p = HTML::TokeParser->new( \$sample_HTML );
my $token;
my $link_count = 1;

while( $token = $p->get_token() ) {
  if( $token->[0] eq 'S' && 
      $token->[1] eq 'a' )
  {
    my $text = $token->[2]->{'href'};
    print "Found link $link_count: $text\n";
    $link_count++;
  }
  if( $token->[0] eq 'C' &&
      $token->[1] eq '<!--ignore-->' )
  {
    while ( $token->[0] ne 'E' &&
            $token->[1] ne 'a' )
    {
       $token = $p->get_token();
    }
  }
}

__output___

%perl ignore_some.pl

Found link 1: http://www.foobar1.com/
Found link 2: http://www.foobar3.com/