When I (Krugos) used to draw my own comics, I penciled a page, then used a marker to make the line art darker, and then inked on a better quality paper using a lamp to see the pencil art behind. Then I would usually color digitally, though a few comics I colored using watercolors.
As for Eli Navarro (the artist I share this account with), he pencils traditionally but sometimes not the way the final page will look like; he may do panels in different pieces of paper and then resize and crop digitally to make the final page. When the pencil work is done, he inks digitally and, if he's doing the colors then he does that also on the PC..