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I am not sure if you still want an answer to your original question but here it is. Even late I had to add my two cents worth because you questions show that you are looking for exactly what I was looking for.
I rooted my Nook STR simply so that I could get Cool Reader. With Cool Reader I get the two things that you were looking for. I have about 2500 books on my Nook. I load them all from Calibre. With Cool Reader I can see lists of series, authors, tags and more. I can also redefine the screen touch points which was very important to me. Sometimes I use my left hand for my ereader and sometimes my right. I have defined all the left and right sides of the screen as page forward when I touch any of those areas. I think I defined one top corner for page back. The other day I was sitting on a train from the airport holding my luggage with one hand and my Nook with the other. I didn't have a choice of hands (my luggage was in the aisle on my right side). With my left hand I could hold the book and turn the page with my thumb. It was extremely convenient. I am very happy with both the organization and the ability to define the screen. There are also buttons to use for when you want. Of course, what makes all this possible is starting with Calibre which is the most outstanding product for ereading of all.
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