Everyone who makes a living through baseball (or someday hopes to) is seeking that extra advantage that will make them stand out. Entire industries have developed around the quest to be stronger, faster, hit farther, and throw harder. The problem is everyone thinks they are a training expert and most don't know the first thing about proper baseball training methods.
A true master and student of baseball training will study the available techniques, take the best, and form them into a comprehensive program. Every good baseball training program contains some form of strength & conditioning. The problem is most baseball-specific training programs are completely off base and cause more harm than good.
This is obviously not what you want and need to improve your baseball performance. The program you choose should include methods that improve balance as well as strength: medicine ball drills, free weights and other dynamic movements are good examples. By approaching your workouts in a more "holistic" (or complete) manner your overall conditioning will improve at the best possible rate while honing your baseball specific muscle groups.
Training on machines is a sure way to train your muscles the wrong way. This may possibly be the worst type of baseball strength training. The goal should be to stand up during your workout and sit as little as possible. Train on your feet so that your body is conditioned to respond while you are on your feet - not sitting.
Another mistake is to train by throwing a heavy baseball or swinging a heavy bat. Again, more damage is done with these techniques and they are not improving your game. It doesn't take much to do these particular techniques incorrectly, and when done wrong they will likely lead to injury.
So in order to maximize your baseball performance, be sure to include as many baseball-specific movements in your training program as possible. Movements in gym workouts should recruit the same joints, muscles and movements that are used in the course of practice or a game. Your baseball training program can make or break you as a baseball player.