Calibre is a great program. But two things about it bother me: it is very slow when it comes to several hundreds of books (haven't tried to add all of my books). The other thing is that it would be the best software if I could actually make it to recognize my books and download the metadata automatically. Yes, I have tried to do it, but it just doesn't recognize my mostly scanned and free ebooks. So I just don't want to enter details for around ten thousands books manually.
However, it does have like a ton of useful features and I use it, but not as my main cataloging software. I use Alfa Manager.
As for the paid vs free software, I think it is comparable to OpenOffice and Microsoft Office. People mainly use the paid version because of the software speed. Although, I'm not sure that's always the case, since many people are actually using Adobe software
.