Hi Paul,

Some of the methods papers also include example clinical applications, e.g. this one has a section on "[apparent fibre density] AFD voxel-based analysis of Motor Neurone Disease"
  http://dx.doi.org/10.1016/j.neuroimage.2011.10.045

This paper uses generalized fiber anisotropy (GFA) to study genetic influences and IQ:
  http://www.ncbi.nlm.nih.gov/pubmed/18979850

This paper, if I have understood it correctly from a quick glance, uses standard FA, but computes it for each of two fitted tensors, and studies first-episode schizophrenia:
  http://dx.doi.org/10.1016/j.mri.2010.10.005

I'm afraid I don't know of any longitudinal work yet, but I believe a couple of groups have some planned...

Best wishes,
Ged