Speaking from the neuroimaging analysis perspective, freesufer/fsl is a great combination and together can cover a great deal of modalities (MRI, DWI, FMRI). There are other popular packages for functional data such as AFNI and SPM. I put in a support ticket for ANTs which started as a nonlinear registration tool but has grown. A newer package for diffusion processing is MRTrix3. For EEG/MEG data you can also use SPM although it is more common to use FieldTrip or EEGLAB (both MATLAB toolboxes). These are all GPL licensed BTW. There is also a great software stack in python found at nipy.org. A good reference for what software people use in the field might be NeuroDebian (http://neuro.debian.net) or NITRC. NeuroDebian will cover a number of packages that are used in computational neuroscience as well such as NEURON. Hope this helps at least for this slice of the medical research software needs.
Thanks for the valuable input regarding the medical image analysis and associated tools. This helps me to understand the current state-of-the-art techniques in medical image analysis and the options to expand our support for the image analysis community on OSG Connect.