Found this work by the Society of Biblical Literature on XML standards for Biblical Citations. They're looking ahead to Xlink/Xpointer, which don't seem well-supported yet, but that's definitely the right direction. 2 Timothy 3:16 gets encoded as "Tim2.3.16": not much different from the traditional convention of using a colon for separating chapter and verse, but necessary because the colon has special status in XML.
One addition for corpus work is obvious: an extra index for words. So Tim2.3.16.2 is a reference to the word "Scripture", the second word in the verse (at least in the ESV and some other versions). Of course, you also need a version identifier to ground this word index: some are listed here, though ESV is not.
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