When I started working with books, I was directed to Calibre for organising books and getting them on the Nook. I downloaded it and tried installing it on Linux and failed miserably. Too many missing dependencies with Slackware. It installed nicely on my MacBook, so I started using it there. It's really good. It's a great way of getting your books from non-official sources, making them look good and getting them on your Nook. But for me it was clumsy having it on the MacBook instead of on my regular desktop (Linux). I was introduced to Sigil - an epub editor. It installed easily on Mac and I used it there.
Recently, I had a look at them both again, and decided to try the Linux download again. What a different experience I had this time. This time there were no dependencies. I think they compiled everything they needed statically into the executable. It installed, it ran, and it's so much better to be able to use it under Linux on my regular desktop.
So I've been doing a lot more with ebooks, experimenting and trying to work out what to do. I'm not going to use Calibre to manage my library. The flat model of showing books is like the iTune model and it's good for 20 or 30 books but after that it sucks. I hate this flat approach. I want a hierarchical organisational structure. Calibre does not have it. However Calibre is wonderful for getting books, setting the meta tags, getting decent covers, checking that they work correctly, seeing how they look. I think Calibre works really well for a lot of people as their final organisational library tool, but I want more.
Getting the books onto my iPad is easy with Dropbox. I put them in my ~/Dropbox directory and pull them off on my iPad. GoodReader will access Dropbox directly, but Stanza will not. However it's just as easy to open the Dropbox app, download the file and direct it into Stanza. Works quickly and very nicely.
However Stanza might not be around for much longer. I've used Stanza on other devices, and it's been great. At some point it got acquired by Amazon, and allowed to languish. It broke for IOS5, but did get fixed. There's no guarantee it will stay available and working. It's a great reader.
I do not have a good workflow yet for processing books. I want to get them in, break them apart, re-apply simpler HTML formatting, add the meta data and a cover, re-build them into epub, and then put them into some organisational structure with easy access. Calibre and Sigil play big roles in this process, but not the final roles. I don't like the HTML formatting that they apply to books, even when you create them from a scanned and OCRed paper book.
Anyway, I will keep experimenting until I find something that works for me.