- An interactive periodic table that would allow you to view physical and chemical properties of any element by touching its chemical symbol.
- A graphical tool for visualizing the kinetics of chemical reactions.
- An app that allows the user to set the dissociation constant of an acid or base to see how that acid/base would look in solution (the higher the constant, the more molecules are dissociated). Could also have a concentration slider control and a pH display.
- An osmosis simulator with controls for setting concentrations and degree of permeability. May have graphical displays showing the change in concentration on both sides of membrane.
- A simulator for studying electrical and concentration gradients across a membrane.
- An interactive biological cell. Tapping on an organelle would give you information about its function, associated pathologies, etc.
I could come up with dozens of more ideas, but that would be a nice start!