The Periodization Bible
This option is based on an article written by Dave Tate called "The Periodization Bible, Part 1". If you havent read it yet, go do so now.
Basically, it takes the Westside approach to lifting, throws out everything about max effort and conjugate method and all that, and just leaves the method for doing accessory work. It says that you should determine your accessory work based on the most frequently-taxed muscles that are used during that exercise. It looks something like this:
Military Press (5/3/1)
Shoulders or Chest 5 sets of 10-20 reps (DB bench, DB Incline, DB Military, Incline press, Dips, Pushups)
Lats or Upper Back 5 sets of 10-20 reps (DB rows, Bent Over Rows, Chins, T-bar Rows, Lat Pulldowns, Face Pulls, Shrugs)
Triceps 5 sets of 10-20 reps (Triceps Pushdowns or Triceps Extensions)
Deadlift (5/3/1)
Hamstrings 5 sets of 10-20 reps (Leg Curls, Glute-Ham Raise)
Quads 5 sets of 10-20 reps (Leg Press, Lunges, Hack Squats)
Abs 5 sets of 10-20 reps (Sit-ups, Hanging Leg Raises, Ab Wheel, DB Side Bend)
Bench Press (5/3/1)
Shoulders or Chest 5 sets of 10-20 reps (DB bench, DB Incline, DB Military, Incline press, Dips, Pushups)
Lats or Upper Back 5 sets of 10-20 reps (DB rows, Bent Over Rows, Chins, T-bar Rows, Lat Pulldowns, Face Pulls, Shrugs)
Triceps 5 sets of 10-20 reps (Triceps Pushdowns or Triceps Extensions)
Squat (5/3/1)
Low Back 5 sets of 10-20 reps (Reverse Hyper, Back Raise, Good Morning)
Quads 5 sets of 10-20 reps (Leg Press, Lunges, Hack Squats)
Abs 5 sets of 10-20 reps (Sit-ups, Hanging Leg Raises, Ab Wheel, DB Side Bend)
You can change exercises however you see fit, but note that this wont make or break your program. One thing that you need to remember is that the accessory work it meant to supplement and strengthen the main movement, not detract from it. If you're continually increasing your weight on shoulder presses, but your military press or bench press arent going up, it might be prudent to consider tapering back on the accessory work, or consider changing your accessory routine entirely.