There's a few different things to create the look. First of all there's a traditional outline effect obviously (just rendering the backfaces slightly extruded).
Then there's the shading. Instead of just calculating the colour based on the normals and textures I use those values and compare with an overlay texture in screenspace coordinates. The Overlay texture has a bunch of lines in different opacity. So when the you have a dark value on the shaded side, all the lines will be visible, if it's partly shaded ony a few lines will be visible. Then there's a variety of shaders with slightly different properties of course.
I've played a few games with some similar effect where the sketch lines just felt like a static overaly, which is why I'm offsetting the texture every few frames, and also I calculate the texture cordinates for the overlay based on each units position, so you don't get the effect of objects moving beneath a static pattern, but it only really works because the camera is 2D and there is little movement in depth and little rotation.
When you play in advanced rendering mode there's another step and some post effects. I then use the alpha channel for all the outlines and shading, and then blur and do some other floaty effects on the colour channels while keeping the lines sharp. This will allow the colouring to flow outside the lines a bit for a bit of a watercolour effect