I'm a bit of a dinosaur who refuses to go with the times, so I still do lineart for In Our Shadow in real media and scan it. I do colour digitally because it's so much easier and ends up looking arguably better. Plus laser effects.
I use Open Canvas for colour and Photoshop for effects, text and detailing.
I do see the super smooth lineart of most fully digital comics and think that looks amazing... but I have tried to do it myself and failed catastrophically.