I've been using BibleWorks 9 for a little more than a year now, so here are my suggestions thus far.
1. Create an option to hide the search window. When I am studying a single passage in depth and am not using the search window very much it would be nice to make full use of my screen real-estate.
2. Single click to update Analysis Window. Holding shift is a little awkward just to move over to scroll through a lexicon entry, apparatus, or manuscript as well as when only updating when shift is pressed, as I still have to move the cursor to get it to update. If there was extended options on this functionality so that one could set it to their preferred method of use beyond using the shift key that would be nice. The most comfortable setting would be to have a single click for Analysis window updates, and a double click for searching.
3. Keep the manuscripts coming. This is definitely my favorite feature of BibleWorks 9, and I would love to see more of it. Papyrus Fragments, and Dead Sea Scrolls would be welcomed additions.
4. More OT study tools. The BHS critical apparatus for one would be quite welcome.
5. Unicode integration. Most Bible scholars are used to typing in Greek and Hebrew using whatever keyboard layout they prefer. It would be nice to be able to search etc. by using your own keyboard layout commands.
6. Custom tabs. Several of the tabs I never use such as Words, Context, or Stats. It would be nice to be able to declutter.
7. More Browse/Analysis windows available on the main screen. This would be similar to the Parallel versions pop-up, but on the main screen and allowing for other features to be integrated as well. Possible set ups could be; two browse windows with different manuscripts in type and manuscript images underneath, multiple translations side by side with the CNTTS apparatus etc. You get the idea.
You could set up BibleWorks such that you start with one window and can add or remove windows. You could have the option of whether the new window is a search, browse, analysis, manuscript window etc. You could designate which windows are linked together through some sort of option setting on each. Along this line it would also be nice to be able to have the pop-up items such as grammars, or maps in-line so that you can see everything at once.
8. Flash Card memory. It would be nice to be able to save your place in the flash card module for what you have already learned.
Overall I have thoroughly appreciated BibleWorks. Out of the different Bible Softwares that I own, I use BibleWorks more by far. Keep up the good work.