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.
* If you don't have any of the Bible software packages, Manuscript Comparator will achieve most of the the results you need.
* If you do own one of the programs, my best advice is to familiarize yourself with the text comparison implementation in that package.
* If you are looking to buy a Bible software program, the text comparison tools will probably not be a deciding factor, but the descriptions I provide here should make you aware of what is possible with each.
I am a long-standing and enthusiastic user of Accordance, but I have occasionally been frustrated by its inability to compare more than two manuscripts or versions at a time. In addition to the tools which Mark mentions, I might also recommend Juxta, a free program which I discovered through my seminar on textual criticism with Prof. David Vander Meulen. It does not yet feature extensive support for non-Roman alphabets, but it allows the user to compare more than two texts at a time and also to quickly and easily collate and create an apparatus for a selected group of texts. Here's a screenshot of a comparison of Romans 5:1-2 between the Westcott-Hort and Nestle-Aland versions (including their punctuation):
I'm planning to use Juxta in a current project involving the earliest witnesses to the Gospel of Mark... I'll be sure to report my results.
Also, one minor note of clarification: at the beginning of his post, Mark mentions that a recent blog post of mine inspired by the debate between Bart Ehrman and James White "notes that the reliability of the Greek New Testament is at least 95% even between between the two most extreme text versions (Textus Receptus vs. Westcott & Hort." As I indicated in my post, that statistic is not mine; it was given by James White, and I have not evaluated it. Mark, however, conducted a statistical analysis (via Logos) that indicated a 93.4 percent agreement between the two, and I'm perfectly happy to accept that judgment. ;-)