Computational

Computational Chemistry Comparison and Benchmark Database - NIST database of small molecules with well established heat of formation, including results from many computational methods, including semiempirical and ab initio with various basis sets.
http://srdata.nist.gov/cccbdb/Default.htm

Computational Chemistry List - A resource for computational chemists. Discussions on chemistry software, data, conferences, jobs, quantum chemistry, molecular mechanics, molecular dynamics, QSAR, molecular graphics, molecular modeling, and associated archives
http://www.ccl.net/chemistry/

Molecular Docking Web - Protein-ligand Docking, structures, bioinformatics, computational chemistry, and drug design resources.
http://www.scripps.edu/mb/olson/people/gmm/

Australian Computational Chemistry Via the Internet Project - A set of web-based teaching modules as well as links to related sites.
http://www.chem.swin.edu.au/

MathMol - Provides students, teachers and researchers the basic concepts in mathematics and their connection to molecular modeling. Links to Software, 3D libraries and tutorials.
http://www.nyu.edu/pages/mathmol/

Molecular Modeling for Organic Chemistry - Summary of lecture course which aims to introduce the hierarchy of computational modeling methods used in Organic Chemistry. Links to background and supplemental information.
http://www.ch.ic.ac.uk/local/organic/mod/

Doubly Nudged Elastic Band Method - A framework for finding transition states based on the nudged elastic band method, balancing accuracy with efficiency.
http://www.trygub.com/DNEBtests/

Cambridge University Silicon Graphics Teaching Laboratory - An outline of a course in computational chemistry. Includes exercises in conformational search, molecular dynamics, visualization, and databases.
http://www.ch.cam.ac.uk/cil/SGTL/

MatHub - Features current and background information about molecular modeling and informatics for chemistry and materials science.
http://www.mathub.com/

Centre for Molecular Modeling - Provides several tutorials related to molecular modeling, directory of software and links to databases.
http://cmm.info.nih.gov/modeling/

QSAR World - Includes brief introductions to concepts in Quantitative Structure Activity Relationship modeling as well as links to relevant literature
http://www.qsarworld.com/

Computational Chemistry and Organic Synthesis - A tutorial intended for experimental organic chemists, with emphasis on computational methods for locating and characterizing transition states.
http://www.cmbi.ru.nl/tutorials/cheminf/mopac/comp.html