Calbre is great for setting up collections. Tags translate into collections (you can disable this for individual tags by putting them in [square brackets], which I do for my workflow tags). So if you have a book tagged "Fantasy" it will show up in a collection of the same name. This means it's easy to put a book into multiple collections, too: just apply as many tags as you need.
One word of warning: it's best to keep all the books in a collection together, either in the internal memory or on the SD or MS card. Otherwise, the collection will be listed twice, once for the books in main memory and once for the books on the card, with a little card icon next to the latter. This clutters up the collection list.
I haven't used the most recent Sony software, as the previous couple of versions gave me a massive allergy to it. But, aside from buying books from the Sony bookstore (and why would you want to do that, they're all DRM-y!) calibre can do anything the Sony library software can do, and (as you know) all sorts of things it could never dream of doing. "Not crashing" being one of the most important ones. I get the feeling that Sony's attitude is "they've got our ebook reader, so they
have to use our software, which means we don't have to do any of the hard stuff like, y'know, making it not suck."
So I'd recommend calibre by all means. And remember: friends don't let friends buy DRM'd ebooks.
