I'm thinking about buying the boxed copy of the game when it releases next year, but I was wondering if it was compatible with the dual shock 3? It's the only controller I have that works on a PC too, and this is the one genre of game that I prefer to play with a controller. 
 
Now if you will excuse me, I think I need to go flog myself for a few hours for just saying I prefer to play a game with a controller over a mouse and keyboard.

If the game supports generic non-xinput controllers, then absolutely. I don't own it on PC yet, but almost all PC games with controller support work with non xinput controllers. But in the cases where that's the built-in only option, the 360 controller emulator seems to do wonders.
 
edit: If you have a fightstick, I'd recommend using that instead for this game.

To be honest, I'm actually doing OK with just the keyboard. Still yet to try a controller.

If you have whatever drivers you might need, try playing the game, if that doesn't work, use something like JoyToKey.  
 
I'm doing all this on a Mac, so I assume you shouldn't have any problems on a Windows computer.

I've been using one of these 360 controller emulation programs. it works great.
 
One tip thought: Hold down the right trigger instead of holding down square to run. It will save your controller some a lot of strain.

Here's a guide on how to make a PS3 controller emulate a 360 controller: http://www.motioninjoy.com/blog/motioninjoy-simulate-xbox-360-controller-virtual-xinput-device     
 
Team Meat said they were going to update controller support for non-360 controllers but I don't they've fully implemented it yet. So you can emulate a 360 controller for the time being. Apparently it works fantastically if you can get it up and running.

I see. I just don't want to buy the game and find out that I can't use the controller with it. I know not every game likes to support a lot of different controllers, and I don't feel like spending $50-$60 just for one game.

Assuming the DS3 supports either the xinput or direct input, then yes, it will work with the game.

 doing OK with just the keyboard.   

I use a Saitek Cyborg.  And it runs fine.  I don't even have the drivers installed to let it recognized as a 360 controller.  (Not that it's worked on any Games for Windows game released in the past couple years anyway.  Stupid Microsoft changing things... and stupid Saitek drivers not keeping up...)
 
Either way, you should look into this.  Works perfect.
http://www.jayceooi.com/2009/01/19/download-xbox-360-controller-emulator-for-pc-games/

I've been using a ps3 controller connected to usb with the xbox360 emulation in DS3Tool so far, it's been pretty good.  I can't imagine playing this game with the keyboard. 
 
Remember to disconnect it in the software and not just pull the plug after you finish playing because I have accidentally turned on my ps3 more than 5 times already when turning off the game