Robin Goodfellow is the first pic I've done without the pen tool. (Well just realized I used it for the highlights on the watch.) Usually I scan the lineart and then use the pen tool for all the colors including the shadows which take on solid shapes giving it a celshaded look.
http://www.deviantart.com/view/15639599/
^ That pic is entirely done with the pen tool. I didn't even ink it before I scanned. Was just a pencil sketch. Took me 4 months of on and off coloring to finish it. Doing line art with the pen tool was painful. Basically with the pen tool I outside each shape I want. I do it very carefully to make the shapes appear round. So imagine each line is an shape that I outlined. Trying to kept the lines even and round was hell. Was scanned in at 720 dpi and I zoom in at 400% for the lines. So when I was working on it, the guy's eyebrow would have taken up my entire screen. If I had a wacom tablet (like that bastard Gabe at Penny-Arcade has) would have been a sinch. Had well over 100 layers.
http://www.deviantart.com/view/9538067/ had 425 layers with a width of over 8000 pixels and a size of over a gig if I remember correctly it making it the biggest piece I've worked on.