Here's two free science-related programs that I found fascinating. Feel free to add to the list.

 

Avida

http://dllab.caltech.edu/avida/

Avida is an auto-adaptive genetic system designed primarily for use as a platform in Digital or Artificial Life research. In lay terms, Avida is a digital world in which simple computer programs mutate and evolve. Avida allows us to study questions and perform experiments in evolutionalry dynamics and theoretical biology that are intractable in real biological system.

 

Celestia

http://sourceforge.net/projects/celestia/

Celestia is real-time 3D space simulation which lets you travel through our solar system and to over 100,000 stars in our neighborhood.

Tesla Map

http://web.tampabay.rr.com/swilson9/teslamap.html

helps with all the mathematical side of building a tesla coil... see the site for details incl. screen shots.