Scriptaculous was made more famous because it became part of Ruby on Rails fairly early on. It has also been integrated in to Seaside. One really nice new feature in this library is the ability to morph the styling of an element from one set of CSS to a new set of CSS. Nice colour cross fading and the like.
The nice thing about all these libraries is that they can work side by side without treading on each others toes. They also compliment each other nicely, providing missing functionality that the others don't have. They also all work really well across different browser implementations - reducing the cost and effort required to make your site work properly.