In my opinion, way too much gets made out of drilling shelf pin holes. I simply use a self-centering drill bit and a 1/2" plywood template with the hole spacing I need. By the time you've made your setup to begin work, I've finished with the entire cabinet and moved on to the next. An entire cabinet can be completed in less than 60 seconds, depending on the number of holes of course.
I use 1/2" thick by 2" wide templates with the holes slightly off-center so I can offset the holes on opposite sides of a partition without the holes intersecting each other. I prefer to drill the holes after the cabinet has been assembled, but it is just as easy to do with un-assembled components too. Part of the reason I prefer to drill the holes after the cabinet is assembled is to ensure that all 4 corners are registered off the same surface. That's not a problem if your cabinets are separate boxes for each opening, but if you build cabinets with multiple openings and dadoed partitions, then it becomes more critical.
I also don't just blindly drill the holes top-to-bottom. No one would ever install a shelf 3" off the bottom of a cabinet, for example. So the first hole is 6 to 8 inches from the bottom, and the top hole is proportionally spaced from the top, depending on the style of the cabinet.
Once you have one template that is carefully made, replicating it in any length is just a matter of using one template to make the next. So I have a whole series of templates specific to various cabinet styles. For example, for an entertainment cabinet, I use a shorter hole spacing to account for keeping the shelves tighter to the contents. I also keep specific templates for all common cabinet heights. That way I don't have to remember when to start or stop drilling holes. I just drill them all for that particular template. (I don't like seeing holes go all the way top-to-bottom. To me, that looks cheap.)
The drill bit below is exactly what I use. It has a 1/4" bit, and a 3/8" collar. Therefore, my templates have 3/8" holes, and their 1/2" thickness is just right to let the drill bit bottom out on the plywood surface to drill the proper depth of hole.
Edit: By the way, I'm sure someone is sitting there scratching their head wondering how a plywood template can be accurate enough to not have the shelves rock. That's the whole point. It doesn't need to be perfect, as long as it is registered off the same surface. The same template hole is used to drill all 4 shelf pin holes for a particular shelf location, so the shelf will never rock. What is more important however, is that all of the holes line up vertically so they don't look sloppy. So when you make your master template, you should use a drill press and fence to ensure that all holes are lined up perfectly with the edge of the template. You can be sloppy on hole spacing without a problem, but if the holes are not perfectly in a line, it will be noticeable.
