I thought there was discussion about being able to rearange bookmarks within a folder in version 4. It seems that the rearanging capabilities are the same as before. Am I thinking of something discussed for 4.1? Or did I read more into the rearanging abilities than was discussed? I would like to move bookmarks up or down within a folder rather than only sorted by books or dates.

Also, I thought there was to be topical notes that aren't linked to a verse where folders and subfolders (similar to the bookmark folders) can be created for them. Is that for a future version, or is it that I didn't see it?

There is a 4.1 beta that has notes not attached to a verse, plus folders for notes.  This hasn't been released in any product yet.

Sorting of bookmarks (or, rather, user-sorting of bookmarks) isn't in any beta yet, but it's on the list of things-to-do.

When you get to the user sorting I like the way you can move entries in the favorites list in the phone application on the phone. If you touch on the far right while in the edit mode you can drag the entry to the desired location. Or perhaps the way you can move the position of icons on the screen.