I start with pencil. Sometimes I ink it with either a marker (of wide variety) or, if I'm feeling serious, a dip pen. Only on rare occasions do I use a brush or brush-pen. For me, a brush always results in far more areas of solid black because it kind of grabs me.
Only after I have taken a photo with my phone do I clean it up in GIMP...with a simple mouse! Fixing exposure (always), using an overlay layer to darken/lighten areas (the camera never takes a consistent tone). Using white to digitally add white highlights is also a common usage.
I would love to be all analog, but try not to get too hung up about it because once its scanned it I see errors and then there's almost no going back.
Throughout the whole process I am the epitome of lazy. Not bothering to erase pencil, clean up smudges etc. I'm sure the lack of discipline shows, but it's just a hobby, and I think of what I'm posting here as a sketchbook while I'm learning the craft. A record of the journey.
You are correct, it's getting harder to tell what is digital, and what is not.