I usually start of with a mechanical pencil sketch on computer paper, then I scan it in, ink in black in photoshop, color in layers below it, then create a layer above the ink with a clipping mask to color the inked lines appropriately.



Sometimes, like my my Laharl Pony or Trotting Mad drawings, I sketch with a Non-repo blue pencil, then use either a mechanical pencil or a soft dark pencil (usually a 6B) to ink. I'll scan that in, then I have some steps to convert that into line art on a separate layer, which I can't remember at the moment because I'm at work - I'll check later.

Other than the examples listed above, I usually do this when I'm doing a digital painting, since I can put that a low opacity above my painting during the early stages so I can still see my sketch to know where everything goes.