Many times while Penetration testing from the Client Network i have came across a situation in which client has an internal proxy server for accessing everything .
I had to do a network scanning for WAN devices using   NMAP through a proxy server and client  was using ISA server as their proxy server  to achieve there is a  tool knows as ProxyChains which  allows to run any program through HTTP or SOCKS proxy

http://proxychains.sourceforge.net/

how to install and configure proxychains

root@bt:~#apt-get install proxychains  (if ur using any debian distro)
root@bt:~#nano etc/proxychains.conf
Than you will see the proxylist where we can add our proxies:

[ProxyList]
# add proxy here …
# meanwile
# defaults set to “tor”
socks4 127.0.0.1 9050

now add ur ISA server proxy server IP like below

[ProxyList]
# add proxy here …
# meanwile
# defaults set to “tor”
192.168.1.13 8080—>ISA server IP
Socks4 127.0.0.1 9050

save and exit

root@bt:~# proxychains nmap -sV WANIP