Some games don't support joysticks, but yet you want to use the PS3 controller with those games.
With a custom profile in MotioninJoy's DS3 Tool, you can map keyboards keys or even the mouse to the buttons and axises on your PS3 controller.
This guide will show you how to do this step by step.
Before you start this guide, make sure of the stuff below with your game:
Start by opening the DS3 Tool and click Create next to the “Custom” option.

You will now be on the Create Custom Profile page.

Yes, this page looks awfully confusing with all the menus, but it's really straightforward.
In each row of the page here, the picture on the far left shows what button/axis of the controller you are configuring.
The left menu lets you configure what the button/axis will do (such as be a button, axis, keyboard key, mouse axis, etc), and the right menu lets you adjust the values that the selected option on the left menu allows.
Below are some sample configurations you can follow along with to get the hang of making a custom profile.
to be written later
Alright, let's say you are configuring a custom profile for a racing game, and you want the triggers (L2 and R2) to be on separate axises so you can have separate gas and brake functions.
Alright, lets say you are configuring a custom profile for a FPS game that doesn't support controllers, only the keyboard.
First you'll want to use the left stick to move your avatar/character right? Usually in PC FPS games, the keys “W A S D” are used to move your character, so here we'll map the left stick to these keys so the left stick will move your character.
Now that you created your profile, you need to save it.
Now that your profile is created, saved, and enabled, you need to test to make sure your profile settings are working correctly. If the settings aren't working correctly, choose different settings for whatever isn't working in the Custom profile, then Save, Enable, and test again until it works right. Most likely you will have some trial-and-error in working with your custom profile, but eventually it will work.