I would stay away from any programs on bodybuilding.com. While that is a great place to get supplements, the info is more geared towards a bodybuilder...and even their baseball programs are generic and more of a bodybuilding style.
There was some good advice in these posts. You can strength train at age 13 and the results can be profound, assuming it's done correctly.
The goals should be to increase neurological efficiency, overall body awareness and power output (athleticism) and conditioning.
It's true that heavy weights simply aren't needed at this age, but that does not mean that "power" movements shouldn't be performed. Exercises such as squats, power cleans, power snatches, push presses, etc should be done, but with a medicine ball and/or a wooden dowel/very light bar and not heavy weights.
The work done now will translate into performance down the road.
Also, you hear much about "balance" training these days. Usually you see someone doing a stupid balancing act on a wobble board or BOSU ball that isn;t reallty doing anything. True is one canot increase balance after puberty. You can increase the ability to right yourself in a certain skill, but your balance ceiling is all but determined by the age of 15.
So at 13 "balance" exercises should be performed. Now this does not mean standing on a balance board. This is done by playing as many sports as possible, performing tumbling exercises, and drills such as med ball drills that force the user to learn how to accept and redirect submaximal objects with maximal force.
I would stay away from plyometric exercises at this point. They are far too taxing on the Central Nervous System (CNS). In addition, plyo's are the most misunderstood aspect in training today and are used as nothing more than a selling tool for most. Jumping over a line 50 times or up and down off a box 50 time is not plyometrics. It's training for an injury and shouldn't be done.
True plyometric training starts off by learning how to land (after all how can you jump if you don't know how to land?) and then progresses from there. True plyometrics involve sets of 1-3 reps, not 100.
Young athletes can build a tremendous amount of usable strength, but as mentioned they will not put on bulk at this age. This, again, is due to the immaturity of their Central Nervous System.
So in closing focus on med ball drills, baseball-specific core drills (not crunches!), conditioning exercises and multi-joint power movements.