The actual list of resources
You can see the sortable and filterable resource index table here.
It is on its own page since it is desirable to display it full-width so that everything has enough room. (Displaying in a narrower-width content section like the one on this page cramps things. The sidebar menu reduces the amount of usable horizontal space, which is more necessary in the case of the table than general text).
How these resources are referenced on this site
One of the sections on the content features page in the write-up about site features and functionality goes into great depth about how this site forms direct links to resources in Bible software programs.
Why the resources are owned in the Bible software programs they are
Buying most things in Logos
Note that some of these resources (the older ones out of copyright) may be found for free on the internet. Purchasing everything in Logos allows for verse tagging, resource syncing, and other things of this sort, which cumulatively save a lot of time in the long run.
I favor Logos over other Bible Software options largely because it has the widest resource selection (in my experience), lets you hyperlink to resources dynamically (as above), and is the only one of the big players to support a full webapp (meaning you can access your library from any computer, so long as you have an internet connection).
Logos also gives you a free $20 credit every year on your birthday, which is nice.
Except for in-line resources, which are in OliveTree
For whatever reason, OliveTree has the best selection of in-line helps, so I own my study Bibles, Bible handbooks, and in-line topical resources (cf. the Thompson Chain Reference Bible) in OliveTree.
Except for Greek manuscript transcriptions, which are in Accordance
I actually use Accordance too, meaning I own things in all three of the "big fish" Bible software programs.
At the moment, Accordance offers the most transcribed textual sources for textual criticism. Both Logos and Accordance have the main critical editions (NA28/UBS5 for the Greek New Testament, BHS/BHQ for the Hebrew Old Testament). Since most of my library is in Logos (including all the lexicons), I run the critical editions in Logos (and also own Metzger's Textual Commentary, the CNTTS apparatus, etc. there). Where Accordance shines is in offering a wider range of transcriptions of actual textual witnesses.
On the Hebrew side of things, you can get both the text of the Leningrad Codex (the main textual witness for the Masoretic text) and also morphologically-tagged transcriptions of the Qumran Cave Scrolls (better known as the Dead Sea Scrolls, or DSS) in both applications, along with the Samaritan Pentateuch. Neither application has transcriptions for Codex Cairensis, the Aleppo Codex, or the Damascus Pentateuch, as far as I know. Since they both fare equally well in Hebrew textual criticism, to keep my library centralized, I own everything in Logos.
On the Greek side of things, you can get the NT Papyri (transcriptions from The Text of the Earliest New Testament Greek Manuscripts - Comfort & Barrett) in both applications, along with Codex Sinaiticus and Codex Bezae. Unfortunately, Logos does not offer transcriptions of Codex Vaticanus or Codex Alexandrinus (two of the important early codices), nor Codex Washingtonianus (later and less important as a witness, but still nice-to-have). Accordance offers transcriptions for all of these texts. Both applications still lack Codex Ephraemi Rescriptus (although the now-defunct BibleWorks had it, and all these others besides).
Since Accordance offers broader support for comparison between Greek textual sources, I own these resources specifically in Accordance. Accordance has some good advanced tools to make full use of these transcriptions for textual criticism, such as automatically highlighting differences and so on. Both applications are plenty powerful in this regard. In fact, since the applications do so well handling parallel texts (hurray, computers!), as long as you use the appropriate tools in these applications, you don't need a separate formal harmony of the gospels (e.g., Synopis Quattuor Evangeliorum). Such a paper resource used to be an absolutely critical resource for deep study of parallel passages in the gospels, but now the same functionality is basically baked right into the software applications.