Photoshop, After Effects, Maya, Houdini, Nuke, UV Layout, ZBrush Rendered in Mental Ray and Mantra
The Knight from concepts through the final 8-Bit version:

The Knight concept for Early Generation:

The Knight concept for Current Generation:

The Enemy from concept to 8-Bit to 16-Bit to 3D:

Breakdown of the Early Generation Style:
Breakdown of the Current Generation Style: