The most popular way to control the lights in the light shows is a DMX. Good basic description of DMX is here: http://www.pangolin.com/LD2000/dmx-about.htm
Windows:
Entec Light Factory: http://www.enttec.com/lightfactory.php ($480/512ch)
Bluelight http://www.innovateshowcontrols.com/x1_overview.php ($400/512ch)
DMX Desk http://www.geocities.com/ph_zone/DMX_Desk/index.html simple, freeware
Open DMX Theater http://dmxtheater.plekkie.net/index.html
FreeStyler (Good) http://users.pandora.be/freestylerdmx/
MagicQ http://www.chamsys.co.uk/
Axis DMX: http://www.axisdmx.com/purchase.html
Linux:
DMX4Linux http://llg.cubic.org/dmx4linux/ driver
Q Light controller, uses DMX4Linux driver http://qlc.sourceforge.net/ 512devices