I was happy to see that Serious Sam 3 BFE (a first person shooter) had controller support. Most Steam games will denote whether a game has controller support or not. Sometimes it may say "Partial Controller Support". I am not certain what that means but some controller support is better than none in my opinion. I took a chance and bought the game. When I fired it up my After Glow Xbox 360 Controller was supported immediately upon turning on the game. This is with a default Ubuntu 12.04.3 installation, it uses the xpad module (driver) and I didn't have to install the xboxdrv module (driver) which is a userspace driver. There are some advantages to using the xboxdrv module but I won't cover those in this post.
Other games I quickly found the same controller did NOT work in, notably all the Source Engine Games by Valve. The ones I tried were Team Fortress 2, Portal, and Left 4 Dead 2 the controller did not work. I tried everything, from opening the console in game and entering "exce 360controller" and "exec 360controllerlinux" to allowing world readable permissions on the /dev/input/event11 device node which is what the controller was plugged into but nothing was working. Well after many hours of googling and trial and error I found what finally solved the controller issue for Valve's Source Engine Games. The original solution has to be credited back to a google post just to give credit where credit is due.
First open the Steam Client and you'll notice that there is a place to click to activate Big Picture Mode, it's located on the upper right side of your Steam Client.