This post isn’t a fair comparison of Bible software, but it is a suggestion that you look into the value of something beyond the free options. If you are in a position to invest financially in software, then Bible software is well worth considering.
There are three “big boys” that I’ll mention.
Logos Bible Software
Available on PC and Mac, Logos offers an impressive array of content. I’ll be honest, I’m still getting used to the pure Bible functions of Logos, as I have been a BibleWorks user for so long (and still reach for it on my netbook at times). But it seems to me that Logos is improving and at least catching up in terms of exegetical function. Where Logos seems to stand alone is in the array of commentaries and research materials you can get on it. My suggestion is to prioritize the quality commentaries and resources so that they are the ones you automatically go to when you are looking at a passage (i.e. there are plenty of resources on Logos that you shouldn’t feel bad about ignoring — it’s still worth the price for the quality ones!).
In simplistic terms, if you want lots of books, go to Logos. If you want to work with the text itself rather than commentaries, especially in the original languages, then BibleWorks is fantastic. It is a PC-based software. (Although some do run it on an emulator on the Mac, I haven’t gone down that route.) Truth is that BibleWorks is probably capable of much that you will never use. I would say that people with any original language knowledge probably need something beyond the free options, and this is definitely one to consider for PC folks. If you don’t use Greek and Hebrew, then BibleWorks will still prove very helpful, but you may find the cost prohibitive (as with all three).
I can’t speak for this one, as I haven’t gone there. Accordance is the Mac-based Bible software. Users I know seem to delight in it, primarily for its intuitive Bible-handling interface, but it also has Logos-like collections of resources that can be added at a cost. I suppose Accordance would argue: what is the point of emulating a PC on a Mac? If you have a Mac, you know how it works, and so do the Accordance folks as they’ve always designed their software for this platform.
For many, these software options represent a luxury that is simply out of reach financially. For that reason I am thankful that the gap between free and expensive is not as big a gulf as it would be in most purchases.