I’ve been using various types of Bible Study software for ten or more years now.
For much of this time, I have been very happy to use a couple of old, but very useful, packages. The first was Quickverse 4 (subsequent versions were completely different and not to my liking at all). Quickverse provided me with a very simple and effective way of annotating Bible verses in order to build up a personal commentary. The second was Bible Illustrator. Although designed (like it says on the tin) as a way of organising sermon illustrations, I found Bible Illustrator to be a fantastic tool for storing and retrieving any text that needed to organised by topic rather than by Bible reference. The tool pieces of software worked together, and, as I say, kept me ‘in business’ for a number of years.
All the time, in the background, I was using in a more limited way packages such as Online Bible and Logos. OLB is good for both recording notes both by Bible reference and by topic, but has various limitations and idiosyncracies. Earlier versions of the Logos software provided access to an ever-growing body of electronic texts (commentaries and other reference material) but had its own quirks and was very limited in what it would let you do by way of creating user-written material.
Enter Logos 4. This has been out for a month or two now. It’s a pretty thorough update and, in addition to letting you access and use all those commentaries and other theological resources that you can purchase, provides an impressive range of Bible study tools.
If you want sophisticated searching, access to a vast range of contemporary biblical and theological resources (many of which are instantly down-loadable), original-language study, high level of customisability, maps and graphs, and much more, then this is the product of choice.