Working on a list of applications (software, apps, or online tools) for making - coding, working with hardware like Makey Makey and Arduino, and 3D printing applications.

Coding/Programming:
Scratch http://scratch.mit.edu/
Tynker http://www.tynker.com/
BYOB/SNAP http://byob.berkeley.edu/
Alice http://www.alice.org/index.php
Daisy the Dinosaur (iOS) http://www.daisythedinosaur.com/
Hopscotch (iOS) http://www.gethopscotch.com/

3D/CAD:
SketchUp http://www.sketchup.com/
TinkerCAD https://tinkercad.com/
123D http://www.123dapp.com/
Blender http://www.blender.org/
Sculptris http://pixologic.com/sculptris/ (takes some work to get into 3D print formats)
Makerbot Makerware http://www.makerbot.com/support/makerware/
3DTin http://www.3dtin.com/
Wings3D http://www.wings3d.com/
FreeCAD http://www.freecadweb.org/
OpenSCAD http://www.openscad.org/
Shapesmith http://shapesmith.net/
Publish Your Design http://www.publishyourdesign.com/

Other:
Twine http://www.auntiepixelante.com/twine/