Visualization software that can run outside the browser:
Jmol(Requires Java)
PyMol(Requires Python)
Note that all of these will be useful for visualizing protein structure if you are planning to work at the interface of chemistry and biology.

2-D drawing programs:
ChemDraw: the standard in the field. OSU has a site license for this commercial software.
JChemPaint (requires Java)

A collection oflinks to online Organic Chemistry resources: Web-ster's Organic Chemistry

IUPAC rules: (see the 1979 recommendations)
Rules for drawing molecules and expressing stereochemical information: (requires either you be on campus or that you use the OSU proxy server)
Experimental data on leaving group ability: (also need on-campus or proxy server access)