I do my inked lines... with ink. Brush pen and real paper, scanned and then finished in Illustrator. Maybe one day I'll get a cintiq (or equivalent) and move to doing things all digital, but for now I like my hybrid process.
I have done some line art in illustrator--the brush tool and width tool both are very helpful for that. But as my process has developed I've been doing more traditional inking. It works and I like it.