I have a paid membership at LibraryThing. I like it a lot. The interface is ugly compared to similar sites and its social networking features are so-so, but its strength lies in its powerful book cataloguing features. Very flexible and customisable when it comes to dealing with metadata or filtering through one's books in their library.
I also like LibraryThing because:
1) the developers are active and fairly involved in the community;
2) it's well integrated with a book-swapping site I use,
BookMooch.
Haven't dabbled much in GoodReads so far, but what I've seen I've liked. GoodReads seems to be more of a 'social networking for readers' website. I avoid Shelfari (yet another book cataloguing/social networking site) out of suspicion of past distasteful marketing practices.