First off - Jmol. I really like Jmol, it is an Open Source java viewer for chemical structures in 3D. It has a number of capabilities, you can rotate molecules on the screen, display electrostatic potentials, bounding boxes, view molecular surfaces, show reaction animation, view orbitals and even upload macromolecules taken from the protein databank!
I am in the process of applying for postdoctoral positions in bio/chemoinformatics.
Below Is a list of some of the software I use and some scripts/programs I have found useful in my PhD. I have also included a list of some of the open source software that I have used through out my project and some useful websites which information on datasets, chemoinformatics papers and academic institutes actively doing research in chemoinformatics.