Understanding Elbow Pain - Part 4: Protecting Pitchers. Cressey is a expert in the field of physical training for amateur and professional athletes. He works with a lot of baseball players and knows what he's talking about. He has a useful blog that I read occasionally, which our high school pitchers might also be interested in.
The article is wordy, but here are essentially Cressey's four primary ways to protect pitchers at any level:
1. Good Mechanics. No two pitchers are alike, but there are certain angles and timing issues to avoid, which exert more stress on the elbow. Visit my Lessons page for additional info on learning proper mechanics at a young age.
2. Avoiding Overuse. This has been discussed by about everyone. See the post below.
3. Long Term Physical Preparation. I think flexibility is most important for youth pitchers, but strength training is beneficial as well.
4. Short Term Physical Preparation. Pitchers should warm up their bodies first, then their arms. And don't forget the stretching and cool down period afterwords.
There's much more in the article, including some good links in each section.