For pretty accurate holes drilled on center,I sometimes take a very slight cut across the bar clamped in the vise in my vertical mill. From there,it is easy to find the center of the narrow flat spot with a center drill and make a good starting hole. Then,without moving the table,except for straight down,put in a drill chuck with a drill in it and complete the job. Recently I made a brass hammer head for a client and quickly drilled the eye out that way. Then,I elongated the hole with an end mill,and put some swag into the hole by hand with a round file. Not talking working to .001" here,but I'll bet the hole wasn't off by more than a few thou. Depends upon your eyeball gauge.
For more critical apps, follow the other suggestions.
One thing i do have is an antique looking rig for holding smaller rods,with a large assortment of hardened bushings. I think it is Swiss. Came in a nice oak cabinet.