Games that are better played with a controller?

Platformers, Racing and Fighting games and that's pretty much it.

Super Meat Boy is a great game to play using a controller. Also had fun with Braid, Fly'n, and Dust: An Elysian Tail.

Sonic Generations, almost every Lego, Castle Crasher, and with big picture is better

Anodyne

A.R.E.S. Extinction Agenda

The Binding of Isaac

Blocks That Matter

Cave Story+

DLC Quest

Fairy Bloom Freesia

Hotline Miami

Jamestown

Offspring Fling

Shank

Shank 2

Sonic Generations

Stealth Bastard Deluxe

Super House of Dead Ninjas

Super Meat Boy

They Bleed Pixels

Castle Crashers and Devil May Cry.

Since I didn't see it mentioned, yet, Jet Set Radio is best played with a controller.

Personally, I enjoyed Assassin's Creed games way more with gamepad than with keyboard.

The Last Remnant, while it can be played with a keyboard assuming you find the on-screen prompt toggle to show keyboard keys instead of controller buttons, the game plays poorly with a keyboard.

Dark Souls, no questions about that.

None, PC master race doesn't need puny controllers to feel special.

You just should be using Keyboard and Mouse for First Person Shooters and point-and-click games. Usually everything else is good with a controller.