I either do this on another copy or over the original pencils. Whenever I can, I like to ink over copies of the pencils printed in blue line. It makes it easier to knock back the pencils when scanning and editing in photoshop so only the inks show up.
I like to use brushes and a variety of brush pens, namely Zebra and Kuretake. But you can get a variety of brush pens from jetpens for a decent price and they even offer free shipping for orders over $25. I use tech pens generally when I need neat straight lines or something. Also, I know plenty of people who like to use crow quills.
For a good number of people, this would probably be the last step, except for lettering. People who can pull off just black and white comics need to have REALLY good spot black placement and generally are pretty good at making different textures as a kind of gray tone.
Either way, the next post will be my last one on the process I go through for comics.