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Calibre by far.
I use the Sony Reader software only to buy books from the Sony store.
Calibre has the advantage of automatically creating collections based whatever data you want. Author, Series, Tags, A custom column. And it can cause the collections to be sorted in any other you like. So Series based collections are sorted in series order. I make Author collections based on a custom column, so I can add a sort order, and I have it sorted by published date. I prefer to read authors in the order they wrote them.
I had Sony Reader mess up my collections and collection order several times. So I stopped using it.
Calibre also allows you to change or add a cover.
With some add ins, it can change which 3 books show up on the home page of the reader, and even change the New tag (turn it off or on).
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