Christine Borgman who presented yesterday at a Harvard iic Colloquium mentioned mentioned some citizen science games that your son’s may be interested in exploring: http://www.galaxyzoo.org/ and http://www.worldwidetelescope.org/

Here are a few resources for middle and high school students interested in computer programming:

Learning Logo Resources: http://www.eecs.berkeley.edu/~bh/. The books themselves are free in electronic form.
StarLogo TNG, which is more aimed at game design and science simulations.
http://education.mit.edu/drupal/starlogo-tng/learn
Scratch fto teach basic programming concepts for the first few weeks in the undergrad CS survey course: http://info.scratch.mit.edu/Educators