SeeSAR Version 4.2 just came out! The main new features are

• You now control when the compute-intense Hyde-calculation runs, this means large sets of molecules can now be loaded, analyzed and processed (e.g. filtering, calculating properties) before the intensive affinity calculations are run.
• Much improved version of grouping all poses of the same molecule

Version 4.2 comes with a load of minor improvements, particularly for the command line use. The full release notes are here.

I've been following this software since it was first released and there is a review here, every update brings useful features. It is well worth downloading the free 1 week trial to have a look at.