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I only started using Calibre after the custom columns were made. Before that, it offered no functionality that I would use (beside the ebook-convert batch process...)
But now, I use Calibre mainly as tool to keep track of reading status and version of my copies (as I generate my own PDFs, I need to reformat every single book and I like to keep track if I've already proof-read a book or not). The reason I couldn't use it before, was the fact that I couldn't save the books where I wanted to. As the BBM doesn't support metadata, I want my books in a fixed folder structure. But, my other two readers don't support folders but do have metadata. But both work differently. So, with plugboards and custom controls, I can add books to all my devices without too much trouble (though, I do have to do the save bit three times for my Mini, as I like the different formats in different folders).
The fact that I still have a folder where I keep my (de-drm'd and drm'd) originals and even a different folder where I keep my sources (which is basically an unpacked epub) makes it a bit more difficult, but the custom controls and plugboards do add a lot of functionality that I'm willing to ignore the fact that it's not the perfect tool for me.
In the end, it's a weighing of the pros and cons. The cons were too heavy for me before, but the custom controls and plugboard tipped the scales towards the pros, especially since I've more than one reader which show their libraries all in a different way...
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