Well, I am sure that others will want to chime in, but for me:
1. The info pane - brilliant addition to be able to quickly see some basic information about a verse, and what resources you have that deal with the verse, and the improving topics database.
2. Research search (used to be search all) is substantially improved in speed, accuracy and display of results.
3. Combined tools. e.g. I have combined WBC OT and NT into a single tool so that anywhere that I go in the Bible I have a comment on a verse.
4. The new library organisation is much nicer. Easier to find resources and is much more customiseable than previously.
5. The new notes are looking really good. The improved formatting options and implementation of Unicode makes them a really useful part of Accordance - and they are on the improve!
6. Did I mention the topic database? :-) and the ability to search by topics.
7. Text suggestions as you type into the search entry box so you can just select from the drop down menu and choose a word or a command. Find it quite useful!
They are the ones I use and can think of off the top of my head. You can find a full list of the improvements here.