Every now and then players choose to play their favorite games with a controller, but there is no controller support given, so what to do?

There is a tool called Xpadder wich allows you to configure you Controller for each and every game. You can bind every Key or complete Key Commands / Combos as you wish. I have used this tool for years and love it.
This Guide will walk you through the process of installing Xpadder and configuring this software for your game.
Personally I use a wireless XBOX 360 Controller with a wireless usb adapter, wich is the best solution for compatibility for each game (most Steam games support the 360 Controller right away without any Xpadder configuration, but sadly not each and every game). Besides this preferable configuration, Xpadder will work the same way for most other Controllers even the cheap and crappy ones :)

Playing System Shock 2 with a controller is a two edged sword, most of the gameplay works pretty well, like in the egoshooter parts and everything else. But the micromanagement in the windows (inventory + map + skills + etc.) is really not made for a controller, but it works fine and after 50 hours of playing SS2 I can say, that for me it was a better gaming experience than playing with mouse+keyboard. After configuring your controller, most of the important stuff is alredy binded to various buttons, so you don't have to fiddle too much in the inventory. But as there is no other way (besides a wireless mouse, wich would be fine) it becomes very convenient very quick.