Isolating mains-powered devices sometimes is tricky, for example in one device of [1] we resorted to specially wound transformers with increased spacing to minimize capacitive coupling to mains/ground, accepting the resulting higher losses in the low-voltage power-supplies.

If you want to research if "ground loops" are indeed of concern, try to inject them artificially (split up protective earth, feed in current from a function generator) and check the influence on your measurement, then you can quantify the "ground loop rejection ratio" of your setup. This will also tell you which frequencies are most susceptible to disturbance in your specific setup.

In your paper, you seem to only have a CCD line camera taking the data, most likely it will be easier to cut open the grounding here, mount it using plastic screws and spacers, if not already done. {EDIT:} ...or not feasible because of the heatsinking...

[1] http://arxiv.org/abs/1302.6092

Agreed, and we've tried that with other USB DAQ systems. The +5 rail is still referenced to the inferior ground. You can split that guy out too, and bring in external power; but then there's the question of the signal lines - to whom are they referenced, and will they function reliably?

It's so much more satisfying to know that you have truly isolated connections than to worry about whether you've gotten a complicated system laid out correctly. I don't trust me to get the details right :).

(As you say, for cleaning up AC from the mains, isolation transformers are fabulous.)