Reviews in Computational Chemistry by Lipkowitz and Boyd is an excellent series of books which does just that. Unlike most review series, it includes introductory and tutorial as well as more advanced material.
The World-Wide Web Virtual Library: Chemistry is an excellent starting place to look for any chemistry related information.
A more general page of links to chemistry resources.
QCPE (The Quantum Chemistry Program Exchange) provides a wide range of computational chemistry software, often free.
NIH has a page on molecular modeling and has a guide to software.
An online-text which discusses aspects of quantum mechanics, the Born-Oppenheimer approximation, and molecular mechanics.
I've had some direct experience with a few software packages:
MSI's Cerius 2 provided an excellent but relatively expensive package which ran on several commercial platforms (SGI, RS6000, and the like).
Hypercube's Hyperchem under Windows on the PC provides excellent capabilities at the price.
CambridgeSoft provides a package that runs on the Mac and under Windows. It is more limited in its modeling capabilities: it can effectively do energy minimizations on structures with perhaps a hundred atoms (their minimizer does only steepest descent). They provide truly excellent facilities for making black & white pictures of molecules, and equally excellent facilities for drawing journal-quality 2-dimensional chemical structures using standard notation.
Gaussian is an ab initio program that usually costs over $10,000 but which is now available on the PC for under $1,000. While it has an antediluvian user interface (designed for punch cards) it is the de facto standard against which competing companies (like the startup Schrodinger) compare themselves and is well known in the computational chemistry literature. They can be reached by e-mail at email@example.com.
While I haven't had direct experience with it, Jay Ponder (who gave an excellent talk on molecular mechanics at the First Foresight conference on Molecular Nanotechnology) has made available a molecular mechanics and dynamics package written in Fortran 77 which is free (including source code). To quote their description:
TINKER is a complete package for performing molecular mechanics calculations. It is intended to serve as a platform for algorithm development and parameterization, while still being efficient enough for most production work. The currently available potentials include MM2 and MM3, AMBER-95, AMBER/OPLS, CHARMM22 and our own TINKER potential. Many other literature potentials can be implemented via external parameter files; parameter sets for ENCAD and MMFF-94 are under development.
Programs are provided to perform many functions including the following: (1) energy minimization over Cartesian or torsional coordinates via conjugate gradient, variable metric or truncated Newton methods, (2) molecular dynamics with periodic boundaries and options to control temperature and pressure, (3) normal mode vibrational analysis, (4) distance geometry including a new, efficient random atom-pair metrization, (5) simulated annealing with a choice of cooling protocols, (6) analysis and breakdown of single point potential energies, (7) verification of analytical derivatives of the standard potential and/or user defined functions, (8) location of a transition state between two minima, (9) free energy perturbation calculations, (10) fitting of intermolecular potential parameters to crystal structure and thermodynamic data, and (11) diffusion equation method and Gaussian density annealing approaches to optimization via smoothed potential energy surfaces.
This list is short and biased, but it should provide a starting point for anyone interested in looking into computational chemistry software.