How to run Telltale games with PS3 controller?
By default, most games do not have controller support. Some of them do, especially newer ones. As time goes on more and more PC games are coming stock with controller support. A majority of them implement it very poorly, while very few actually have good (and customizable) controller support.
I recommend using a third party solution globally regardless of what game you play (whether it has support or not) for one very important reason. The solution I will present to you, gives you 100% customization options, full support for all games, and comes pre-stocked with different "profiles" you can find to fill out controller controls per game. Most are done by other gamers who have built them on their own while playing the game, and they get community ratings and supports so you can find out which ones are widely used, and liked.
The app I recommend can be found here: http://pinnaclegameprofiler.com/
It does cost money, but it is the best on the market. I have used controller support apps before that were free, and they never had the same level of customization, or power. They also don't feature the nicely built profile system to easily get new profiles instead of having to build the profile controls yourself.
I personally stopped using the controller for most games on PC (even though I use an Alienware laptop). I started realizing that with a little bit of getting use to, most of the time the keyboard/mouse combo works the best, as that was how they were originally designed.
Although some games (Sleeping Dogs for example) have horrible PC/Moues controls. Most do the control schema very well.
Good luck, and let me know if you need more advice!
Edit:
Below are a few profile links for some of the games you mentioned, and some other telltale games.
http://pinnaclegameprofiler.com/pc-controller-support/alpha-gamepad-joystick/xbox-360-ps3-psx-etc/rogue-legacy
http://pinnaclegameprofiler.com/pc-controller-support/alpha-gamepad-joystick/xbox-360-ps3-psx-etc/dont-starve