I'd load up with...

Commercial software:
  • Geometer's Sketchpad - can be used for more than just Geometry, too
  • Fathom - dynamic data -- can be used in cross-discipline projects, too
  • Logger Lite/Pro - science folks likely know about this software already
  • For writing tests, etc. use MathType
Free software:
  • Geogebra
  • Any blogging platform - ask students to explain some of the big ideas of the class.  Karl Fisch is doing this with his students. 
Big teaching ideas:
Anything you'd add to the list?