The following is from http://wilhelmsen.wordpress.com/2009/10/18/connect-to-wpa-with-terminal-ubuntu

assuming your wirelesscontroller is named “wlan0″

First, stop network-manager:

sudo /etc/init.d/networkmanager stop

Then make a config for wpa_supplicant:

wpa_passphrase "ssid" "password" > wpaconfig
sudo wpa_supplicant -iwlan0 -cwpaconfig

When you see from the output that you are connected, press [ctrl+z] to run wpa_supplicant in the background temporarily and type $bg to run it in background.
To be assigned to a IP:

sudo dhclient wlan0

Currently unrated