We say two Bible verses are linked when verse A and verse B are related to each other. Williams Bible Links™ collects Bible verse links cited in public domain works such as Bible commentaries and cross reference collections.
The system then tallies how many citations each link has in our sources. This is a measure of how much consensus there is that the link is important. The more citations, the more authors thought the relationship between two verses to be interesting.
The abridged version displays the top-cited references for each verse.
The unabridged version divides the references for each verse into levels according to citation count, with level 1 containing the top-cited references, level 2 containing the next tier down, and so on. Sometimes a level is empty. That is normal, as level 1 appropriates references from lower-tier levels if necessary in order to make a full page.
The system only uses links confirmed with two or more citations. This is to protect from off-the-path references and typos. Of course, this means some perfectly good references are missed. Live by the citation count, die by the citation count.
The strategy is that as more sources are added, these missed links will be confirmed by additional citations. Also with more citations available, the system will likely be able to boost increasingly-relevant references into the abridged version and level 1 of the unabridged version.
Currently we have identified three million "links" but the system only uses one million of them -- the confirmed links. Each link results in two cross reference entries: Lookup verse A points to cross reference B, and lookup verse B points to cross reference A. So the unabridged version actually has two million confirmed cross references. The abridged version has close to half a million.
I have learned to have a degree of humility when I do not see a connection between my lookup verse and a particular reference for it. More than once I have said to a friend "I don't see how this reference is related to the verse I looked up" only to have my friend exclaim in essence "Wow! They saw that connection!" Sometimes it helps to look at the context of both verses to see the relationship.
The system attempts to group each lookup verse's references into topics, using network community detection techniques.