A hidden gem in BibleWorks is the “MacDonald Greek Transcription.”
BibleWorks comes with sentence diagrams for the Greek New Testament. They are also useful and look like this:
The MacDonald transcriptions above, however, replicate something I haven’t seen in any other Bible software (EDIT/UPDATE: Logos has a “clausal outlines” module, minus the color coding), which is the sentence flow method of representing and visualizing a sentence. He uses color coding and spacing to line up parallel ideas and repeated words, making them easier to see than in just the text or even the diagrams.
It’s a great way to get at the motifs and important words of a given passage. And I’d forgotten about it until recently, but am now using it most weeks in sermon preparation.
The full title of the resource above is Syntactic and Thematic Greek Transcription of the New Testament, by William Graham MacDonald, 2008. BibleWorks is available here. Its full contents list is here.
Words on the Word 
In Logos, look for Dean Deppe’s “Clausal Outlines of the Greek New Testament”. There are NA27 and an SBLGNT editions. They don’t use color, but they do structure the text, line up related components, etc. Note that Logos’ sentence diagrammer can also be used to structure the text in this way instead of a traditional stick diagram.
Thanks, Rick! I was looking through the Logos pages and forums to see if there was anything, and noticed that you can make your own, but didn’t know about Deppe. I just see it as part of the (erstwhile top-secret?) Biblical Languages package in L5. Is it coming available separately any time soon? I find that method a great way to engage the biblical text.
Ah–I see it is in the L4 Biblical Languages module, too. Made the update in the body of the post.
Nice! I wish they had this in Accordance.
Me too! Maybe they will in the future.