Andrew Dalke has just released fmcs-1.0. It finds a maximum common substructure of two or more structures. Some of the features are:

• handles 1,000s of structures
• several different atom and bond comparison schemes
• modifiers to require ring bonds only match ring bonds, or that incomplete rings are not allowed in the MCS
• user-defined atom class typing through isotope labels (SMILES) or through an SD tag field
• uses an exact solution to find a maximum common substructure
• eports the current best solution if the timeout is reached

The software is distributed under the 2-clause BSD license and available for no charge from https://bitbucket.org/dalke/fmcs/downloads/fmcs-1.0.tar.gz

You must have the Python bindings to RDKit in order to run fmcs.

Usage details are in the README, shown also in the project page at:  https://bitbucket.org/dalke/fmcs/