I'm very happy with Moon+ Reader Pro on my 3rd gen. Fire. It has a great pdf plugin and a very good library/shelf management plugin - it's a virtual separate book collection from the one baked into the Fire OS interface.
(And I mention pdf because that's what I mostly read in it these days - everything else gets converted (in Calibre, on Linux, like in your case) and sent to my Paperwhite.
I also tried FBReader, but its shelf/library management was useless. No experience with KOreader.
Oh, and I also have Bluefire installed - this is mainly for ADE DRM compatibility (which Moon+ lacks). No Overdrive here (Spain), and all public digital libraries use ADE DRM.
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