CheMCS Suite
If you are looking for quick exact MCS calculations on molecules, then look no further!
The CheMCS (or Chemical Maximum Common Subgraph) tools were developed from my PhD project with Professor Peter Willett and Dr John Holliday at the University of Sheffield. Of main note is the ability to quickly calculate the MCS on several molecules quickly, whilst yielding more geometrically sensible MCSs which show a more intuitive similarity.
The MCS in this context is shown on pairwise molecular comparisons in this GUI tool - 5 x 100 molecules in this case. It can be used to visualise similarity between molecules. However, the MCS in general can also be used for molecular alignment (copying of coordinates), virtual screening, and mapping reactants and products in chemical synthesis. Tools for these alternative functions I may produce and release in the future.
For larger scale comparisons, please refer to the CLI equivalent.