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I'm sure others have touched on these points already, I guess I'm just throwing in my two cents. If I had my choice I would preferably only use one application to manage my reading device and ebook library, but unfortunately I do have several texts that require authorization which does mandate the use of Sony's library application.
I have found that extremely large texts, e.g. the NIV Holy Bible, which if it has not been paginated using Sony's library software will cause my Sony PRS-505 device to crash. I have also found that by not using the Sony library software for transfer, even the smallest files have caused reduced battery life because the device itself is then forced to paginate the LRF files after they are transferred. This may seem trivial, but the more often you are required to charge up your battery, the shorter the life expectancy of your device's internal non-replaceable battery.
As for Calibre, well, it is a wonderful application. I use it to manage all the tags and metadata of my ebooks after I transfer them to my device, as well as the general organization of my digitized texts on my personal computer. Secondly I love Calibre for the wonderful ability to import news feeds. If you havn't already done so, perhaps you might try giving the "bookit" Firefox extension a try. It is the perfect compliment to Calibre by allowing you to save web pages and articles directly to your Calibre library from a single click.
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