Myself I would do it like this, I think it is more readable than regexing it all in one go

#!/usr/bin/perl

use strict;
use warnings;

use CGI qw/:standard/;
use CGI::Carp qw(fatalsToBrowser);

print header();

local $/="";

while (<DATA>) {
    s/\n/,/sg;
    s/\"//g;
    my ($name, $number, @bits)=split /,/;
    my $string;
    for (@bits){
        $string.=", \"".$_."\"" if $_=~/^CN=/;
    }
    print "$name, $number$string\n";
}


__DATA__
DHCP Administrators,2,"CN=May Mary,OU=Enterprise Admins,Users,DC=INTER
+NETNET,DC=com
Domain Admins,Users,DC=INTERNETNETCOM,DC=com",,

DnsAdmins,2,"Enterprise Admins,Users,DC=INTERNETNET,DC=com
CN=Arth Gure,OU=Marketing,OU=User Accounts,DC=INTERNETNET,DC=com
Domain Admins,Users,DC=INTERNETCOM,DC=com",,

AS400 Query Database,2,"CN=Joe Car,OU=Systems/Operations,OU=MIS,OU=Use
+r Accounts,DC=INTERNETNET,DC=com
CN=Ricrad Tallar,OU=Systems/Operations,OU=MIS,OU=User Accounts,DC=INTE
+RNETNETCOM,DC=com",,

Deptpar Access,8,"CN=John Class,OU=Marketing,OU=User Accounts,DC=INTER
+NETNET,DC=com
CN=Judy Lipa,OU=Marketing,OU=User Accounts,DC=INTERNETNET,DC=com
CN=George Grey,OU=Marketing,OU=User Accounts,DC=INTERNETNET,DC=com
Artur More,OU=Marketing,OU=User Accounts,DC=INTERNETNET,DC=com
CN=Raimun Sirilo,OU=Executive,OU=User Accounts,DC=INTERNETNET,DC=com
CN=Amilcar Ove,OU=Marketing,OU=User Accounts,DC=INTERNETNET,DC=com
Daniel Santos,OU=Executive,OU=User Accounts,DC=INTERNETNET,DC=com
CN=Paula Corte,OU=Executive,OU=User Accounts,DC=INTERNETNET,DC=com"

Human_Resources,3,"CN=Katarine Gilly,OU=Executive,OU=User Accounts,DC=
+INTERNETNET,DC=com
CN=Chris Head,OU=Human Resources,OU=Finance & Administration,OU=User A
+ccounts,DC=INTERNETNET,DC=com
CN=Susany Cadru,OU=Human Resources,OU=Finance & Administration,OU=User
+ Accounts,DC=INTERNETNET,DC=com"

# results (without the CGI)
DHCP Administrators, 2, "CN=May Mary"
DnsAdmins, 2, "CN=Arth Gure"
AS400 Query Database, 2, "CN=Joe Car", "CN=Ricrad Tallar"
Deptpar Access, 8, "CN=John Class", "CN=Judy Lipa", "CN=George Grey", 
+"CN=Raimun Sirilo", "CN=Amilcar Ove", "CN=Paula Corte"
Human_Resources, 3, "CN=Katarine Gilly", "CN=Chris Head", "CN=Susany C
+adru"
[download]

Cheers,
R.