Dear Matt,
PDS format contains raw data which have been only pre-processed. This is why you get stripes, noise, and distortions in your THEMIS images from the PDS. If you want to get some "nice" data, you have to make some processing on them using the USGS ISIS-3 (
http://isis.astrogeology.usgs.gov). ISIS is not really easy to learn alone, but it is actually the only software able to deal whith rigourous camera model and so on. Then from ISIS, it is possible to export into ENVI format (e.g., binary raw). There are also some gdal script able to export mapping info into ENVI header format.
If you only need to visualize the images, you just have to download the png/tiff from the themis website, and then display them with envi. These png file are generally radiometricaly calibrated, but not always map projected. You can, if so deal with MOLA by using some Tie points, but this is tricky.
To my mind, the best way is ISIS.
Good luck!
A.