It seems like it was heavily designed to let people use a 360 controller on the PC version as opposed to any other third party or PS3 ones. My computer detects the PS3 controller under game controllers, but for the life of me I can't figure out how to make Batman: AA play ball.
do you use your ps3 controller for other games on your pc?
as a last resort there is a program called pinnacle game profiler that lets you use any controller with any game (as long as your pc detects your controller of course), but that can be hard to set up with the analog sticks.
Honestly i'd just go and buy a wired 360 controller, there are tons of games that come with a preset for it and, personally, i prefer the 360's controller to the ps3's --- Some people just need a swift kick in the ass XBL:Vote Palpatine | PSN: Orange Julious | Steam: Spacepope
I got my PS3 controller to work with my PC just by Googling for some drivers and a prog that lets your assign the buttons, it works, but you need to assign almost every game manually and the analog sticks were extremely tricky with the sensetivity. It was a while ago so probably there is a better version released. Google is your friend.
As for alternatives - I hate Xbox controllers, just cant stand them, probably because I used PS all my life, so the natural choice for PC was Logitech Rumblepad 2, I picked it up for 14 quid online and have been using it almost on all non fps games. The good things are that its cheap and works like it should, shaped exactly like a PS controller with the only difference is that the bottom triggers are not springy like on PS3 so its more like a PS2 controller, but it doesnt play any role for me. If you really need wireless theres that version as well.