I have a little experience with strength & conditioning for baseball. My younger brother was drafted out of HS by the Royals last summer. He's an outfielder. Anyway, like many have mentioned before any lifts that promote hip drive/leg&core strength are good for baseball players. For throwing though, you have to get your arm in shape. All the shoulder/bench/etc. work will not help much if you don't throw. We would go through 45 minute throwing sessions a few times per week during off-season. Start just by throwing short distances and gradually work out to long toss (as far as possible while still able to reach a target) then throw at that distance for a few minutes. From long distances, it's natural for most players to put quite a bit of arch on the ball, that's fine. After a few minutes of toss at a close to max distance, gradually work your way back to a short distance (90 ft or so). This is where all the work comes in. Try to keep the same velocity on the ball that you were applying from the longer distances but work on releasing the ball later in the movement. Think of "pulling" the ball down from the release point of a max distance throw, to allow for accuracy and less arch on each throw as the distance decreases. This really helped my brother. He didn't pitch much but it also increased his mound speed by a consistent 7-8 mph.
Lengthy explanation. I hope it helped.