Brushes are preferred by many old school comic book artists due to the amount of control a person can achieve with a brush. A brush can be pressed down to create a thick fat line as well as be lifted nearly off the page to create tiny, thin detail lines. Brushes also can be dipped into a well of ink and reloaded easily. Brushes ink hair especially well. The light strokes that can be made wider or thinner with a simple change of pressure are excellent at creating subtle curls and displaying the reflection of light or sheen in a character's hair.
Pens are popular because they are easier to use. One of the problems with pens, though, is that they cannot create the multitude of strokes and shapes in the way a brush can. However, a pen does produce a hard and solid line, and many artists prefer this to the softer curvier strokes of a brush. When using pens, use only ink well pens and avoid all ballpoint, felt tip and Sharpie-style pens. These pens are not designed to ink line work the way an old fashioned ink well pen is.
Structures that contain minute mechanical parts work are excellent subjects for pen inking. Shapes such as gears, buttons, rivets, wires and pistons all need a fine level of technical detail, and an ink pen can create consistent straight lines to achieve this effect.
These days, many artists are inking their work digitally using a stylus and digital drawing tablet. One of the advantages of this is that once the stylus and tablet are purchased, there are never any brushes to wash, ink to replace or messy spills that could ruin hours of work. One of the disadvantages of inking digitally is that it further separates the artist from his medium and can sometimes produce flat or unexciting ink lines.
Pencil line art is scanned into a computer and then a digital painting program such as Corel or Photoshop is used to create the ink job. A separate layer is created so that all the ink work can be done on one layer while leaving the original untouched. You can also select from a myriad of different brush and pen styles and the pressure sensitivity of the stylus can be used to create thick or thin lines in the same way you would with a traditional brush.