Did you know that the Congregation for the Clergy (the Holy See) offers a free biblical analysis software?
It is free to download at http://www.clerus.org/bibliaclerus/index_eng.html
This is another great resource. Although, the English version is not as complete as the French or Italian there are still 100’s of books cross referenced to respective passages of scripture.
You can read the bible in parallel modern or ancient (Hebrew, Greek or Latin) languages. You can search the bible for particular words or themes. You have extensive Church Father works cross referenced (especially St. Augustine & St. Chrysostom), the Catechism of the Catholic Church, Homilies from Pope John Paul and Pope Benedict and numerous other documents. (even more if you can read French or Italian)
If you are looking for a great bible software do look up particular themes in the bible or are looking to see how particular verse have been understood this website/software is a great free resource.
Although the software may not be as user friendly as I would like it, I cant argue because it is free. When I have told others about this website, I was amazed how often this gem was a hidden one. I hope it become less hidden with the publication of this review.
(Also it has Vatican II documents cross reference as well for great ease in showing their deep scriptural foundation!!)