"Full length", "serious" and "youth company" is not a particularly common combination.  (Most of the serious plays performed by that agegroup have the actors playing adults.)

At a pinch, Thorn by Kent Mick might fit the bill.

There is indeed a stage version of Lord of the Flies.  I directed the North American premiere years ago at The Haverford School, though admittedly I wish I could have done my own adaptation.  Of course, the problem with that show is that it's all male, which isn't necessarily desirable to many youth theatre producers.

Cheers,
Jon

If you are looking for musicals try here

http://www.spotlightmusicals.com/

Midsummer Night's Dream is a good one.