I think the method mostly depends on what kind of comic you want to do, what fits the best.
As for my comic I use Paint Tool Sai, it's a great tool, the lineart looks much better, you can do painterly style more easily than in Photoshop, it's much more painting and drawing oriented program, but with less effects and no text tools. But Paint Tool Sai 2 is coming! And also it's much cheaper 
I don't like scanned lines as well, I only do sketches on paper and the line on PC, but lately I do everything on PC, it's much faster.
My method for my comic is quite simple. I sketch up the panels (I have a template PSD since I use the same format), lineart with pencil tool, select areas to color with magic wand tool to lay down base colors, and add additional colors with the pencil tool. Color over the lineart, it gives more life to it, and then I add some other elements, like drop shadow, etc. Then I add the text and speech bubbles in PS.
And if you are interested in more painterly or detailed style you can hit up Deviantart, there are lots of great tutorials there.