For me, the main one is the ability to create custom shelves. Unless Shelfari has recently added that? I like being able to categorize my books however I want. Also, Goodreads gives me a lot of reading stats - like how many books I read in the year and how many of those I rated however many stars, how many were in what genres, etc. I don't think Shelfari has this. GR also have challenges you can join or set for yourself. And while Shelfari goes have groups/book clubs, I feel GR's are more active and better designed to encourage group reads.
For example, this group on GR has monthly group reads which can be displayed as "currently reading" right on the home page of the group with the designated time period the group will be reading that book: http://www.goodreads.com/group/show/22454-historical-fictionistas
- it also links to the section of the group discussions where the book will be discussed. Shelfari does have "group shelves" and one of which is "we're reading" but it does not display on the home page nor does it allow the group to specify when they are reading it or have a link to the discussion of the book. I gather because of this, no one seems to use it to organize group reads.
Lastly, I find GR generally has a lot more book ratings and reviews and the more feedback I get on a book, the better I can make a decision on whether to buy it.
Fair enough if most of these things don't appeal to you but they are both supposed to be social networking sites and I feel GR has more social interaction. For me, the only thing Shelfari did better was allow me to easily import my whole Kindle library - that WAS very convenient and allowed me to easily test out Shelfari with my library. But since I joined GR before I started reading Kindle books, I never needed that feature on GR anyway.