Well, now that SCSaunders put me on the spot....
BibleWorks plays well with Logos/Libronix using the external links manager. Check these threads
HERE and
HERE.
(The only thing that does not seem to pass through well from BW to Logos is Hebrew words.)
What this means is that you can use the speed and the text-centric focus of BW7 to do work and then quickly jump over (using a right-click) to the secondary resources in Logos.
It does not work very easily to move from Logos to BW7.
As for coordination with NotaBene, I don't think either BW7 or Logos have built in macros (as they both do for working within MS Word). On the other hand, copy/paste works fine from BW7 to NotaBene. BW7 allows you to export text in Unicode, so it's good to go. You won't get the automatic footnote that Logos generates when you copy/paste text (the default setup), but I usually don't need it for biblical text anyway.
Post here if you have more specific questions, and check my blog, especially
THESE POSTS where I often compare/contrast Logos and BW7.