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Some linux systems, like Ubuntu, cannot properly authenticate against a Microsoft ISA proxy server.

To get through a Windows Proxy server, you need to install NTLMAPS.

If you are using Ubuntu, you can download NTMLAPS from here:  http://packages.ubuntu.com/

To download NTLMAPS, you will need to use a web browser that can authenticate properly, thankfully the new versions of Firefox (that are usually pre-installed with the operating system) can get through the proxy. First setup Firefox with the proper proxy settings for your network, then browse to: http://packages.ubuntu.com. Click on the version of ubuntu you have installed, then click on the Web Software section, then on ntlmaps in the list.

Click on all in the download table at the bottom of the page, and choose a mirror.

Once downloaded, you can either install it by double clicking on the .deb file, or install it from the terminal:

sudo dpkg -i ntlmaps_0.9.9.0.1-6_all.deb

If you install the package via the gnome package installer, a prompt will appear asking for proxy server details. Leave the listen port at 5865, type in the proxy server you need to connect to, correct port, the windows domain, username and password.

Once configured, ntmlaps should be ready to use. Basically ntlmaps is a proxy server that runs on your pc, that can be connected to without usernames/passwords, that uses it's configured settings to connect through your windows proxy.

To use your ntlmaps proxy

To test out your new proxy, try changing your Firefox settings. Open Firefox, and set your http proxy to 127.0.0.1 using port 5865

You should now be able to access the internet using Firefox without putting in a username and password. Once you have confirmed that that is working, put these proxy details into the Synaptics Package Manager so you can install new programs and keep your system up to date.

System -> Administration -> Synaptics -> Settings -> Preferences -> Network:
Manual proxy configuration: 127.0.0.1 port 5865 (no authentication)

You can also use ntlmaps to enable apt-get to work through the proxy:

Make a file: /etc/apt/apt.conf and add the line:
Acquire::http::proxy "http://127.0.0.1:5865";

Save the file, then run "apt-get update".
 

Ref:http://ubuntuforums.org/showthread.php?t=96802&page=3