Well, there are still pieces of your script missing, so I'm not sure I've captured all of the functionality, but try this...

#!/usr/bin/perl

  use strict;
  use warnings;
  use DBI;

  my $alertstable = $ARGV[0] || 'alertstable';

  my $dbh = DBI->connect("DBI:mysql:database=dbname;host=sqlhost",
                           'username','password',
                          {'RaiseError'=>1});


  my $sth=&Do_SQL("Select * from bademails ORDER BY ID DESC");

  while (my $pointer = $sth->fetchrow_hashref) {
     my $bademail = $pointer->{'email'};

     my $sth2=&Do_SQL2("Select * from $alertstable where email LIKE '%
+$bademail%'");

     while (my $pointer2 = $sth2->fetchrow_hashref) {
    
          my $item = $pointer2->{'type'};
        my $alertype = $pointer2->{'alertype'};
        my $emaillist = $pointer2->{'email'};
        my $ID = $pointer2->{'ID'};



        my @emails = split /~~~/,$emaillist;
          my @goodmails = ();
        foreach my $address (@emails) {

            print "$ID<Br>\n";

               if ($address ne $bademail) {
                 push @goodmails,$address;
               }
        }
        if (scalar(@goodmails)) {
            my $newlist=join('~~~',@goodmails);
            $dbh->do("UPDATE $alertstable SET email='$newlist' WHERE t
+ype='$item' and alerttype='$alertype';") || die $dbh->errstr;
            print "Updated $ID<Br>\n";
        }
     }
    
  } # end while

  $dbh->disconnect;


sub Do_SQL{
  my ($SQL)=@_;
  my $sth;

  eval {
    $sth = $dbh->prepare($SQL);
  }; 

  # check for errors
  if($@){
    $dbh->disconnect;
    print "Content-type: text/html\n\n";
    print "An ERROR occurred! $@\n";
    exit;
  } else {
    $sth->execute;
  } 
  return ($sth);
}
[download]

You'll need to fix up the connect code to reflect your username and password for the database, and it was not clear what $alertable ever got set to, so make sure it is right.

Scott