Calibre 4.0
Full disclosure: I'm a sql & emacs geek so that may warp my views on interfaces. I suspect there are a lot of features that are used by no more than 5-10% of users, but we'd scream bloody murder if they were taken away. No two of my heavy Calibre user friends use exactly the same set of features and we're always swapping tricks. Calibre does a decent job for so many use cases that I'm not sure there's any way to have a completely coherent UI that covers them all. That doesn't mean it's not krufty and occasionally frustrating, but I've no exaggeration never seen an alternative that did even 20% of what I wanted.Calibre can seem pretty overgrown and I used for years without missing features like search-based virtual libraries, but now an ebook management app that doesn't let me slice and dice with that kind of power. For me it's a mix of how easy it is switching between tabbed views like new last 30 days, unread (custom tag automatically added on import), various reading lists from the Reading List plugin, author sets I tend to read together, missing metadata, etc. and the composability of virtual libraries.When you combine virtual libraries with the slightly misleadingly named FanFicFare plugin's metadata it's a lot easier to keep track of both original[1] & fan fictions from dozens of sites (out of several hundred supported) and separate it out from regular books.  Similarly the Reading List & Import List plugins are great for pulling in info from outside calibre, but they need a lot of the features that people generally ignore to do their jobs.On the flip side most people don't seem to use multiple real libraries and they are great for topic-specific book collections or when I really don't want to see a book again, but don't want to just delete it.Even simple things like being able to arbitrarily color column text based on filters I ignored until I realized lets me set the titles of all books missing a description red. It makes cleaning up my library easier, but nothing else I've tried has a similar features.[1] https://github.com/JimmXinu/FanFicFare/wiki/SupportedSites
It's the only thing that makes reading fiction from spacebattles.com not soul-destroyingly annoying.