Central Atom Quandary is a great simulation for students to understand how atoms will be arranged in a molecule. This document is modified from the PHet teacher documents at http://phet.colorado.edu/en/simulation/build-a-molecule.
The American Chemical Society presented this activity at a NSTA convention and it was great at showing why the bonds are at particular angles.
Source: American Chemical Society
This PhET simulation will help students determine if a molecule is polar or not. The document is taken from the http://phet.colorado.edu/ website teacher page. The molecular polarity simulation will help student understand the uneven distribution of charge is key in determining polarity.
Source: http://phet.colorado.edu from the teacher documents portion
