Actually, I don't use painted textures at all. It is really less time-consuming for me to model all details and assign to them simple matrials (diffuse+specular). When I need tiled/grainy/noisy material I usually use procedural maps (tiles/cellular/noise etc) for diffuse and sometimes bump channels.
There are no tricks in rendering process either. You just need a set up with ortogonal camera and default lights.
To achieve "pixelated" look I use very sharp AA filter such as Catmull-Rom. You can try to render without AA, but in this case you will need to pay much more attention to the size of details (I'll give you some examples below).
Then, I overpaint renders in photoshop to add some details & textures, clean edges etc.
There is example of final render just before overpaint: imgur.com/AsY3oZ7

Example renders with catmull-rom AA: imgur.com/An8O1ij
and without AA: imgur.com/k0R0DKN

And the last thing: all models I make for this kind of work are very simple and intended only for the render from one ortogonal view, thus they usually don't have backfaces and any details that will be hidden from camera: imgur.com/aHe5B83