Weightlifting for baseball players used to be a taboo topic many years ago because the old school thought process was that football players lifted weights, not baseball players. Coaches thought lifting would make their players tight and limit their throwing and swinging capabilities. In reality, lifting improperly can cause players to lose flexibility and increase their risk of injury. There is also the fear that players will not settle for just being stronger, but will in fact want to be bigger as well which may lead to poor decision making in terms of choice of exercises, frequency, volume, and supplementation.
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Given the choice between multi-joint -- compound -- and isolation exercises, the multi-joint movements should take priority. These are movements where your body is using multiple joints and muscles to successfully complete the exercise as opposed to isolation exercises that work just one muscle at a time. Think of it this way, bodybuilders need to work every muscle independently to get the most out of it for showcase purposes. Athletic movements usually require a series of muscles working in unison for successful execution. The best compound movements to use are squats and / or lunges (total lower body), dumbbell bench press (chest, shoulders, triceps), pullups (back and biceps), deadlifts (entire body). Isolation exercises like calf raises (lower leg) and wrist curls/wrist extensions (wrists and forearms) are also essential, just be sure not to over work those smaller muscle groups.
With the use of compound exercises and a few isolation moves mixed in, you can train your entire body with a single weight training session. The sessions can be completed in less than an hour and can be done twice to three times per week with at least one day of rest between workouts. Remember, rest between workouts is extremely important to the muscle building process. Working out provides the stimulus for muscles growth while rest actually allows your muscles to adapt.
There are two phases to a complete workout schedule and each one determines the volume of training you will follow. Your offseason training phase should be used to gain more strength and power while performing very little baseball specific drill work. During this phase more weight, higher sets (four to six) and fewer reps (three to six) are required. The in-season phase is more for maintenance than anything else. You are heavy into your baseball specific drill work so your weight will be drastically lighter, sets lower (one to three) and reps higher (10 to 15).
Your rotator cuff should be trained as part of your regular workout schedule. These tiny muscles should be trained for longevity and not strength. You should not be using more than five pounds or so when performing these exercises if you are using free weights. Preferably rubber tubing or resistance bands should be used if they are available to you. Internal and external rotations, full can and empty can raises are effective exercises to properly train your cuff.
Blast that Core
Of all the areas trained for baseball, your core is probably the most important. Any motion where you are bending, twisting or turning requires your core to function properly. Planks are a great staple for core work and Russian twists are an excellent way to work your core through its full twisting range of motion. A medicine ball can be used for the Russian twists as a way of adding extra resistance.