Each program has its strengths and weaknesses. Manuscript Comparator does the best job of displaying differences, but it lacks the NA27, and results cannot be saved. Accordance does a good job of display and creates useful lists of differences, but only two texts at a time can be compared. BibleWorks has the most versatility, but it is difficult to save results. Logos has the most texts available for comparison and results export easily, but one must get accustomed to the way it displays differences
I think many people do these type of comparisons. It would be interesting to hear what our readers think about the methodology and results?
One important thing is to get the software to disregard some features that are insignificant from the genealogical perspective (e.g., editorial features such as moveable nu, etc).
In the comment section I pointed Hoffman to the software Collate and Anastasia which are more suitable for advanced manuscript comparisons and the production of critical apparatuses. These tools are used for the NT transcript prototype (INTF, Münster) and the forthcoming digital NA28. I used Collate 2.0 for my comparison of 560 MSS in Jude. Read more about those tools here. BTW, Anastasia and Collate have their own blog nowadays (but it seems not to be updated very often).
In this connection I should also mention the on-line software LaParola which allows for comparisons and includes a vast amount of editions and manuscripts. It is also possible to insert the whole on-line site into BibleWorks.